bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing Interventions Aimed at Improving Influenza Vaccination Coverage Among Vulnerable Populations: A Systematic Review and Meta-Analysis Protocol
Authors: Wu Pei Chen , McPherson Lyn , Lambert Stephen B , Wnukowski-Mtonga Peter , Lennox Nicholas G , Ware Robert S 
Published: March 2021

ABSTRACTBackgroundInfluenza is a major contributor to global disease burden. Vaccination recommendations specifically target populations at increased risk of serious influenza sequelae. The aim of this study is to conduct a systematic review and meta-analysis to evaluate the effectiveness of different quality improvement interventions to increase vaccination rates in high-risk populations.MethodsRandomized and nonrandomized studies with concurrent control groups will be identified. Interventions to increase vaccination rates will be categorized by strategy type. Overall intervention effects will be calculated using random effects models. Study quality will be assessed using a modified Cochrane Risk of Bias tool.
Development of Equine Immunoglobulin Fragment F(ab’)2with High Neutralizing Capability against SARS-CoV-2
Authors: Gupta Divya , Ahmed Farhan , Tandel Dixit , Parthasarathy Haripriya , Vedagiri Dhiviya , Sah Vishal , Krishna Mohan B , Daga Siddarth , Khan Rafiq Ahmad , Kondiparthi Chiranjeevi , Savari Prabhudas , Jain Sandesh , Daga Jaya , Reddy Shashikala , Khan Nooruddin , Harshan Krishnan Harinivas 
Published: March 2021

ABSTRACTThe ongoing pandemic, COVID-19, caused by SARS-CoV-2 has taken the world, and especially the scientific community by storm. While vaccines are being introduced into the market, there is also a pressing need to find potential drugs and therapeutic modules. Remdesivir is one of the antivirals currently being used with a limited window of action. As more drugs are being vetted, passive immunotherapy in the form of neutralizing antibodies can provide immediate action to combat the increasing numbers of COVID-positive cases. Herein, we demonstrate that equines hyper-immunized with chemically inactivated SARS-CoV-2 generate high titers of antibody with a strong virus neutralizing potential. ELISA performed with pooled antisera displayed highest immunoglobulin titer on 42 days post-immunization, at 1:51,200 dilutions. F(ab’)2immunoglobulin fragments generated from the pools also showed very high, antigen-specific affinity at 1:102,400 dilutions. Finally,in vitrovirus neutralization assays confirmed that different pools of F(ab’)2fragments could successfully neutralize SARS-CoV-2 with titers well above 25,000, indicating the potential of this strategy in treating severe COVID-19 cases with high titers. The F(ab’)2was able to cross neutralize another SARS-CoV-2 strain, demonstrating its efficacy against the emerging viral variants and the importance of this approach in our efforts of eradication of COVID-19. In conclusion, this study demonstrates that virus-neutralizing antibodies raised in equines can potentially be used as a treatment regimen in the form of effective passive immunotherapy to combat COVID-19.
ChexMix: A Literature Content Extraction Tool for Bioentities
Authors: Yang Heejung , Park Beomjun , Park Jinyoung , Lee Jiho , Jang Hyeon Seok , Lee Namgil , Yoo Hojin 
Published: March 2021

AbstractBiomedical databases grow by more than a thousand new publications every day. The large volume of biomedical literature that is being published at an unprecedented rate hinders the discovery of relevant knowledge from keywords of interest to gather new insights and form hypotheses. A text-mining tool, PubTator, helps to automatically annotate bioentities, such as species, chemicals, genes, and diseases, from PubMed abstracts and full-text articles. However, the manual re-organization and analysis of bioentities is a non-trivial and highly time-consuming task. ChexMix was designed to extract the unique identifiers of bioentities from query results. Herein, ChexMix was used to construct a taxonomic tree with allied species among Korean native plants and to extract the medical subject headings unique identifier of the bioentities, which co-occurred with the keywords in the same literature. ChexMix discovered the allied species related to a keyword of interest and experimentally proved its usefulness for multi-species analysis.
Chromosomal rearrangements with stable repertoires of genes and transposable elements in an invasive forest-pathogenic fungus
Authors: Demené Arthur , Laurent Benoît , Cros-Arteil Sandrine , Boury Christophe , Dutech Cyril 
Published: March 2021

AbstractChromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity has been often reported in Fungi, which may explain their apparent ability to quickly adapt to new environments.Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in detail for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de novo whole-genome assembly obtained from a new method of DNA extraction and long-reads sequencing Nanopore technology obtained from a Japanese isolate sampled in the native area of the species. The comparison with a recently published reference genome revealed stable gene and transposable elements (TEs) repertoires. We also showed that theC. parasiticagenome is lowly compartmentalized, with a poor association between TEs and genes, such as those potentially involved in host interactions (i.e., genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high-quality assembled genomes, and questions the role of structural variations in the invasive success of this fungal pathogen species.
DEVELOPMENT OF A SOYBEAN MATURITY PREDICTION MODEL FOR SOYBEAN GROWN IN AFRICAN ENVIRONMENTS
Authors: Marcillo Guillermo S. , Martin Nicolas F. , Diers Brian , Da Fonseca Michelle S. , Leles Erica 
Published: March 2021

AbstractTime-to-maturity (TTM) is an important trait in soybean breeding programs. However, soybean is a relatively new crop in Africa. As such, TTM information is not yet well defined as in other major producing areas. Multi Environment trials (MET) allow breeders to analyze crop performance across diverse conditions but also pose statistical challenges (e.g. unbalanced data). Modern statistical methods, e.g.. Generalized Additive Models (GAM), can flexibly smooth a range of responses while retaining observations that could be lost under other approaches. We leveraged 5 years of data from a MET breeding program in Africa to identify the best geographical and seasonal variables to explain site and genotypic differences in soybean TTM. Using soybean-cycle features (minimum temperature, daylength) along with trial geolocation (longitude, latitude), a GAM model predicted soybean TTM within ± 10 days of the average observed TTM [days post-planting]. Further, we found significant differences between cultivars (p<0.05) in TTM sensitivity to minimum temperature and daylength. Our results show promise to advance the design of maturity systems that enhance soybean planting and breeding decisions in Africa.
Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples
Authors: Nadel Brian B. , Oliva Meritxell , Shou Benjamin L. , Mitchell Keith , Ma Feiyang , Montoya Dennis J. , Mouton Alice , Kim-Hellmuth Sarah , Stranger Barbara E. , Pellegrini Matteo , Mangul Serghei 
Published: March 2021

AbstractEstimating cell type composition of blood and tissue samples is a biological challenge relevant in both laboratory studies and clinical care. In recent years, a number of computational tools have been developed to estimate cell type abundance using gene expression data. While these tools use a variety of approaches, they all leverage expression profiles from purified cell types to evaluate the cell type composition within samples. In this study, we compare ten deconvolution tools and evaluate their performance while using each of eleven separate reference profiles. Specifically, we have run deconvolution tools on over 4,000 samples with known cell type proportions, spanning both immune and stromal cell types. Twelve of these represent in vitro synthetic mixtures and 300 represent in silico synthetic mixtures prepared using single cell data. A final 3,728 clinical samples have been collected from the Framingham Cohort, for which cell populations have been quantified using electrical impedance cell counting. When tools are applied to the Framingham dataset, the tool EPIC produces the highest correlation while GEDIT produces the lowest error. The best tool for other datasets is varied, but CIBERSORT and GEDIT most consistently produce accurate results. In terms of reference choice, we find that the Human Primary Cell Atlas (HPCA) and references published by the EPIC authors produce accurate results for the largest number of tools and datasets. When applying deconvolution to blood samples, the leukocyte reference matrix LM22 is also a suitable choice, usually (but not always) outperforming HPCA and EPIC. Running time varies substantially across tools. For as many as 5052 samples, SaVanT and dtangle reliably finish in under one minute, while slower tools may require up to two hours. However, when using custom references, CIBERSORT can run very slowly, taking over 24 hours to complete for large datasets. We conclude that combining the best tools with optimal reference datasets can provide significant gains in accuracy when carrying out deconvolution tasks.
The ubiquitous terpene geosmin is a warning chemical
Authors: Zaroubi Liana , Ozugergin Imge , Mastronardi Karina , Imfeld Anic , Law Chris , Gélinas Yves , Piekny Alisa , Findlay Brandon L. 
Published: March 2021

AbstractKnown as the smell of earth after rain, geosmin is an odorous terpene detectable by humans at picomolar concentrations. Geosmin production is heavily conserved in actinobacteria, myxobacteria, cyanobacteria, and some fungi, but its biological activity is poorly understood. We theorized that geosmin was an aposematic signal used to indicate the unpalatability of toxin-producing microbes, discouraging predation by eukaryotes. Consistent with this hypothesis we found that geosmin and the related terpene 2-methylisoborneol reduced predation ofStreptomyces coelicolorandMyxococcus xanthusby the bacteriophagousCaenorhabditis elegans. Predation was restored by the removal of both terpene biosynthetic pathways or deletion of theC. elegansASE sensory neuron, and resulted in the death of the nematodes. Geosmin itself was non-toxic. This is the first warning chemical to be identified in bacteria or fungi, and suggests molecular signalling affects microbial predator-prey interactions in a manner similar to the well-studied visual markers of poisonous animal prey.
Cell-specific alterations inPitx1regulatory landscape activation caused by the loss of a single enhancer
Authors: Rouco Raquel , Bompadre Olimpia , Rauseo Antonella , Fazio Olivier , Thorel Fabrizio , Peraldi Rodrigue , Andrey Guillaume 
Published: March 2021

AbstractMost developmental genes rely on multiple transcriptional enhancers for their accurate expression during embryogenesis. Because enhancers may have partially redundant activities, the loss of one of them often leads to a partial loss of gene expression and concurrent moderate phenotypic outcome, if any. While such a phenomenon has been observed in many instances, the nature of the underlying mechanisms remains elusive. We used thePitx1testbed locus to characterize in detail the regulatory and cellular identity alterations following the deletionin vivoof one of its enhancers (Pen), which normally accounts for 30 percent ofPitx1expression in hindlimb buds. By combining single cell transcriptomics and a novelin embryocell tracing approach, we observed that this global decrease inPitx1expression results from both an increase in the number of non- or low-expressing cells, and a decrease in the number of high-expressing cells. We found that the over-representation ofPitx1non/low-expressing cells originates from a failure of thePitx1locus to coordinate enhancer activities and 3D chromatin changes. The resulting increase inPitx1non/low-expressing cells eventually affects the proximal limb more severely than the distal limb, leading to a clubfoot phenotype likely produced through a localized heterochrony and concurrent loss of irregular connective tissue. This data suggests that, in some cases, redundant enhancers may be used to locally enforce a robust activation of their host regulatory landscapes.
CASPAM: a triple modality biosensor for multiplexed imaging of caspase network activity
Authors: Habif Martín , Corbat Agustín A. , Silberberg Mauro , Grecco Hernán E. 
Published: March 2021

AbstractUnderstanding signal propagation across biological networks requires to simultaneously monitor the dynamics of several nodes to uncover correlations masked by inherent intercellular variability. To monitor the enzymatic activity of more than two components over short time scales has proven challenging. Exploiting the narrow spectral width of homoFRET-based biosensors, up to three activities can be imaged through fluorescence polarization anisotropy microscopy. We introduce CASPAM (Caspase Activity Sensor by Polarization Anisotropy Multiplexing) a single-plasmid triple-modality-reporter of key nodes of the apoptotic network. Apoptosis provides an ideal molecular framework to study interactions between its three composing pathways (intrinsic, extrinsic and effector). We characterized the biosensor performance and demonstrated the advantages that equimolar expression has both in simplifying experimental procedure and reducing observable variation, thus enabling robust data-driven modelling. Tools like CASPAM become essential to analyze molecular pathways where multiple nodes need to be simultaneously monitored.
Complex landscapes partially mitigate negative pesticide effects on tropical pollinator communities
Authors: Obregon Diana , Guerrero Olger R. , Stashenko Elena , Poveda Katja 
Published: March 2021

AbstractLand-use change and pesticides have been identified as two of the main causes behind pollinator decline. Understanding how these factors affect crop pollinator communities is crucial to inform practices that generate optimal pollination and ensure sustainable food production. In this study, we investigated the effects of landscape composition and pesticide residues on bee communities and their pollination services inSolanum quitoense“lulo” crops in Colombia. On 10 farms, located along a gradient of landscape complexity that varied from 0.15 to 0.62 in their natural habitat proportion, we characterized the bee community visiting the crop, and carried out pollination experiments with bagged and open inflorescences to later estimate fruit set, weight, and diameter at every site. Additionally, we performed pesticide analysis on collected anthers through liquid chromatography to estimate pesticide risk coming from the crop fields using hazard quotients (HQ). Bee abundance and species richness decreased with increased HQ, but these negative pesticide effects were less detrimental in farms with higher natural habitat proportions. However, this buffer effect was lost at sites with very high HQs. Imidacloprid was frequently found in the anthers and there were extremely high concentrations in some farms (0.6 to 13063 μg/kg), representing the molecule of greater risk for bees in this context. Pollinator’s importance to crop yield was demonstrated in the exclusion experiments, where we found a reduction in fruit set (51%), weight (39%), and diameter (25%). We found a significant effect of bee richness on fruit set, while landscape composition and HQ had no significant effect on fruit set, suggesting that the last two factors do not affect yield directly, but indirectly through a decrease in pollinator diversity. Our results provide novel evidence that the natural habitat loss due to the expansion of pastures for cattle ranching and pesticide residues in anthers reduce bee diversity and abundance in this Andean cropping system, but strategies to protect and restore natural habitat can help to buffer, until certain levels, these negative effects.Highlights- We explored how landscape composition and pesticide residues impact bee communities and pollination services inSolanum quitoensecrops.- As the proportion of natural habitat in the landscape increased, bee richness also increased. While as pesticide hazard quotients inS. quitoenseanthers increased, bee diversity and abundance decreased.- The natural habitat surrounding farms mitigates the negative pesticide effects on bees when hazard quotients are low/medium, but not when they are high.-S. quitoensecrops are highly dependent on bees for optimum yield.
Subthreshold repetitive transcranial magnetic stimulation drives structural synaptic plasticity in the young and aged motor cortex
Authors: Tang Alexander D , Bennett William , Bindoff Aidan D , Bolland Samuel , Collins Jessica , Langley Ross C , Garry Michael I , Summers Jeffery J , Hinder Mark R , Rodger Jennifer , Canty Alison J 
Published: March 2021

AbstractBackgroundRepetitive transcranial magnetic stimulation (rTMS) is a non-invasive tool commonly used to drive neural plasticity in the young adult and aged brain. Recent data from mouse models have shown that even at subthreshold intensities (0.12 Tesla), rTMS can drive neuronal and glial plasticity in the motor cortex. However, the physiological mechanisms underlying subthreshold rTMS induced plasticity and whether these are altered with normal ageing are unclear.ObjectiveTo assess the effect of subthreshold rTMS, using the intermittent theta burst stimulation (iTBS) protocol on structural synaptic plasticity in the mouse motor cortex of young and aged mice.MethodsLongitudinalin vivo2-photon microscopy was used to measure changes to the structural plasticity of pyramidal neuron dendritic spines in the motor cortex following a single train of subthreshold rTMS (in young adult and aged animals) or the same rTMS train administered on 4 consecutive days (in young adult animals only). Data were analysed with Bayesian hierarchical generalized linear regression models and interpreted with the aid of Bayes Factors (BF).ResultsWe found strong evidence (BF>10) that subthreshold rTMS altered the rate of dendritic spine losses and gains, dependent on the number of stimulation sessions and that a single session of subthreshold rTMS was effective in driving structural synaptic plasticity in both young adult and aged mice.ConclusionThese findings provide further evidence that rTMS drives synaptic plasticity in the brain and uncovers structural synaptic plasticity as a key mechanism of subthreshold rTMS induced plasticity.
Cooperative herbivory between two important pests of rice
Authors: Liu Qingsong , Hu Xiaoyun , Su Shuangli , Peng Yufa , Ye Gongyin , Lou Yonggen , Turlings Ted C. J. , Li Yunhe 
Published: March 2021

AbstractNormally, when different species of herbivorous arthropods feed on the same plant this leads to fitness reducing competition. We found this to be uniquely different for two of Asia’s most destructive rice pests, the brown planthopper and the rice striped stem borer. Both insects directly and indirectly benefit from jointly attacking the same host plant. Double infestation improved plant quality, particularly for the stemborer because the planthopper fully suppresses caterpillar-induced production of proteinase inhibitors. It also drastically reduced the risk of egg parasitism, due to diminished parasitoid attraction. Females of both pests have adapted their oviposition behaviour accordingly. Their strong preference for plants infested by the other species even overrides their avoidance of plants already attacked by conspecifics. This uncovered cooperation between herbivores is telling of the exceptional adaptations resulting from the evolution of plant-insect interactions, and points out mechanistic vulnerabilities that can be targeted to control two major pests.
Factors Shaping Young and Mature Bacterial Biofilm Communities in Two Drinking Water Distribution Networks
Authors: Cheng Dan , Leifels Mats , Miccolis Carlo , Wuertz Stefan , Thompson Janelle R. , Szewzyk Ulrich , Whittle Andrew J. 
Published: March 2021

AbstractThe presence of biofilms in drinking water distribution systems (DWDS) can affect both water quality and system integrity; yet these systems remain poorly studied due to lack of accessibility. We established two independent full-scale DWDS Testbeds (A and B) on two different campuses situated in a tropical urban environment and equipped them with online sensors. Testbed B experienced higher levels of monochloramine and lower water age than Testbed A within the campus. Based on long amplicon-sequencing of bacterial 16S rRNA genes extracted from the mature biofilms (MPB) growing on pipes and young biofilms (YSB) growing on the sensors, a core community was identified in the two testbeds. The relative abundances of operational taxonomic units at the family level, includingMycobacteriaceae, Methylobacteriaceae, Rhodospirillaceae, Nitrosomonadaceae,andMoraxellaceae,were consistent for MPB and YSB on each campus. The MPB community was found to be influenced by conductivity, sample age, and pipe diameter as determined by both canonical correlation analysis and fuzzy set ordination. MPB displayed higher α-diversity based on Hill numbers than YSB; in general, second order Hill numbers correlated positively with conductivity and sample age, but negatively with ORP and nitrite.Pseudomonasspp. together withBacillusspp. likely initiated biofilm formation of YSB on Testbed A under conditions of reduced monochloramine and high water age. Significant levels of orthophosphate were detected in YSB samples at two stations and associated with higher levels of stagnation based on long-term differential turbidity measurement (DTM). Orthophosphate and DTM may act as indicators of the biofilm growth potential within DWDS.Highlights- Established two testbeds to study biofilms in full-scale distribution system- Biofilms on pipes and sensors had core community- Temporal effect and higher α-diversity for biofilms on pipes- Water chemistry was related to biofilm community differencesGraphical Abstract