bluuebunny/crossref_metadata_2025_split huggingface dataset:
Process optimization for atrial fibrillation ablation
Authors: Boehmer Andreas A , Summ Alena , Vila Steffen , Rothe Moritz , Nussbaum Elena , Zezyk Celine , Dobre Bianca C , Kaess Bernhard , Ehrlich Joachim R 
Published: March 2022

Abstract

Aims
In the light of an increasing prevalence of atrial fibrillation (AF) and growing evidence for the superiority of early invasive rhythm control, the demand for ablation therapy is rising. Accordingly, ablation centres will have to maximize their capacity by either adding electrophysiology laboratory resources or optimizing process management. In order to optimize process management, we applied “Lean Six Sigma” method to a single ablation center. We compared procedural parameters, acute efficacy and safety of cryoballoon pulmonary vein isolation (cryoPVI) before and after modifications.

Methods and results
Patients (n = 713) undergoing cryoPVI (108 before and 605 after process optimization) were analysed. Within 3 years of process optimization, electrophysiology laboratory occupancy time (150.7 ± 44.4 vs. 94 ± 22.1 min, P &lt; 0.001), procedure time (84.5 ± 21–47.4 ± 12 min, P &lt; 0.001), left-atrial dwell time (53.9 ± 18.4–31.9 ± 9.9 min, P &lt; 0.001), and fluoroscopy time (15.8 ± 5.1 vs. 6.2 ± 2.8 min, P &lt; 0.001) decreased. Contrast dye use (116 ± 35 vs. 27 ± 15 mL, P &lt; 0.001) and radiation dose (893 ± 1078 vs. 253 ± 249 cGy cm2, P &lt; 0.001) were reduced by ∼77 and ∼72%, respectively. There was no difference in safety endpoint occurrence (3.7 vs. 1.5%, P = 0.11).

Conclusion
The process optimization of cryoPVI for AF therapy using the ‘Lean Six Sigma’ method significantly increases efficiency without compromising patient safety.
Industrial R&D and national innovation policy: an institutional reappraisal of the US national innovation system
Authors: Shaikh Ibrahim A , Randhawa Krithika 
Published: March 2022

AbstractStudies highlight how the once envied US national innovation system (NIS) is now showing signs of slowing down. In this article, we unpack this issue from an industrial R&D perspective. First, we highlight that open innovation (OI) practices (i.e., external sources and markets for technologies) have increased the rate of inventive activity in the current wave of industrial R&D, but financialization skews the firms’ focus on short-term profits and shareholder value maximization. When OI intersects with an institutional context that propagates such shareholder-centric governance of R&D, three social costs are incurred by the US NIS: (i) irrational relationship between risks and rewards, (ii) weak antitrust and intellectual property (IP) rights that result in a lack of business dynamism, and (iii) austerity and weak demand-side policies. We contend that these social costs tilt the R&D trajectory toward incremental R&D at the expense of the blue-sky science needed to retain US leadership in technological innovation. Second, we document three social benefits that public-sector R&D agencies generate for the US NIS: (i) undertaking a technology brokerage role, (ii) creating radical R&D markets, and (iii) embracing stakeholder governance. We emphasize how a hidden “entrepreneurial network state” subtly creates and shapes breakthrough R&D and markets for private sector firms but cannot recoup the rewards for society due to political rhetoric that favors incumbent market power. Third, we recommend both incremental and radical policies to drive institutional reforms that promote a stakeholder-centric form of R&D governance so that the future wave of industrial R&D creates value for society. Overall, we draw attention to the role politics plays in industrial R&D and the US NIS and how small adjustments in institutional dimensions and governance modes can impact the US R&D trajectory and competitiveness.
Multiple Profile Models Extract Features from Protein Sequence Data and Resolve Functional Diversity of Very Different Protein Families
Authors: Vicedomini R. , Bouly J.P. , Laine E. , Falciatore A. , Carbone A. 
Published: March 2022

AbstractFunctional classification of proteins from sequences alone has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases. The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of the evolution of living organisms and for biotechnological applications. ProfileView is a sequence-based computational method, designed to functionally classify sets of homologous sequences. It relies on two main ideas: the use of multiple profile models whose construction explores evolutionary information in available databases, and a novel definition of a representation space in which to analyze sequences with multiple profile models combined together. ProfileView classifies protein families by enriching known functional groups with new sequences and discovering new groups and subgroups. We validate ProfileView on seven classes of widespread proteins involved in the interaction with nucleic acids, amino acids and small molecules, and in a large variety of functions and enzymatic reactions. ProfileView agrees with the large set of functional data collected for these proteins from the literature regarding the organization into functional subgroups and residues that characterize the functions. In addition, ProfileView resolves undefined functional classifications and extracts the molecular determinants underlying protein functional diversity, showing its potential to select sequences towards accurate experimental design and discovery of novel biological functions. On protein families with complex domain architecture, ProfileView functional classification reconciles domain combinations, unlike phylogenetic reconstruction. ProfileView proves to outperform the functional classification approach PANTHER, the two k-mer-based methods CUPP and eCAMI and a neural network approach based on Restricted Boltzmann Machines. It overcomes time complexity limitations of the latter.
Cnot8 eliminates naïve regulation networks and is essential for naïve-to-formative pluripotency transition
Authors: Quan Yujun , Wang Meijiao , Xu Chengpeng , Wang Xiaoxiao , Wu Yu , Qin Dandan , Lin Yuxuan , Lu Xukun , Lu Falong , Li Lei 
Published: March 2022

Abstract
Mammalian early epiblasts at different phases are characterized by naïve, formative, and primed pluripotency states, involving extensive transcriptome changes. Here, we report that deadenylase Cnot8 of Ccr4-Not complex plays essential roles during the transition from naïve to formative state. Knock out (KO) Cnot8 resulted in early embryonic lethality in mice, but Cnot8 KO embryonic stem cells (ESCs) could be established. Compared with the cells differentiated from normal ESCs, Cnot8 KO cells highly expressed a great many genes during their differentiation into the formative state, including several hundred naïve-like genes enriched in lipid metabolic process and gene expression regulation that may form the naïve regulation networks. Knockdown expression of the selected genes of naïve regulation networks partially rescued the differentiation defects of Cnot8 KO ESCs. Cnot8 depletion led to the deadenylation defects of its targets, increasing their poly(A) tail lengths and half-life, eventually elevating their expression levels. We further found that Cnot8 was involved in the clearance of targets through its deadenylase activity and the binding of Ccr4-Not complex, as well as the interacting with Tob1 and Pabpc1. Our results suggest that Cnot8 eliminates naïve regulation networks through mRNA clearance, and is essential for naïve-to-formative pluripotency transition.
Differential Virulence Contributions of the Efflux Transporter MexAB-OprM in Pseudomonas syringae Infecting a Variety of Host Plants
Authors: Helmann Tyler C. , King Dana M. , Lindow Steven E. 
Published: March 2022

Efflux transporters such as MexAB-OprM contribute to bacterial resistance to diverse antimicrobial compounds. Here, we show that MexB contributes to epiphytic and late-stage apoplastic growth of Pseudomonas syringae strain B728a, as well as lesion formation in common bean ( Phaseolus vulgaris). Although a ∆ mexB mutant formed fewer lesions after topical application to common bean, these lesions contain the same number of cells (105 to 107 cells) as those caused by the wild-type strain. The internalized population size of both the wild-type and the ∆ mexB mutant within small samples of surface-sterilized asymptomatic portions of leaves varied from undetectably low to as high as 105 cells/cm2. Localized bacterial populations within individual lesions consistently exceeded 105 cells/cm2. Strain B728a was capable of moderate to extensive apoplastic growth in diverse host plants, including lima bean ( P. lunatus), fava bean ( Vicia faba), pepper ( Capsicum annuum), Nicotiana benthamiana, sunflower ( Helianthus annuus), and tomato ( Solanum lycopersicum), but MexB was not required for growth in a subset of these plant species. A model is proposed that MexB provides resistance to as-yet-unidentified antimicrobials that differ between plant species. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Temporally Regulated Plant-Nematode Gene Networks Implicate Metabolic Pathways
Authors: Mishra Shova , Salichs Oscar , DiGennaro Peter 
Published: March 2022

Root-knot nematodes (RKN) (Meloidogyne spp.) constantly communicate with their host to establish and maintain specialized feeding cells. They likely regulate this interaction by monitoring host biology. As plant host biology is influenced by light and gene expression varies correspondingly, RKN gene transcription and biology likely follow similar patterns. We profiled RKN transcripts over a period of 24 h and identified approximately 1,000 differentially expressed genes (DEG) in nematode and model host Medicago truncatula, with the majority of DEG occurring in the middle of the dark period. Many of the plant DEG are involved in defense-response pathways, while the nematode DEG are involved in establishing infection, suggesting a strong host-nematode interaction occurring during the dark. To identify interacting genes, we developed a plant-nematode gene network based on DEG signals. The phenylpropanoid pathway was identified as a significant plant-nematode interacting pathway, representing four of 33 genes in the network. We further examined if this pathway interacts similarly in another host, tomato, by quantifying phenolic and flavonoid compounds produced by this pathway. Phenolic compounds showed a significant increase in production during the day in uninoculated plants as compared with during the night. However, during the dark period, there was an increase in flavonoid content in infected plants when compared with uninfected controls, indicating potential host defense mechanisms active during the height of nematode activity at night. This study elucidated cross-species interacting pathways that could be targeted to develop novel management strategies to these important pests.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Effects of Macroautophagy and Mitophagy on the Pathogenicity of Fusarium graminearum
Authors: Chai Xicun , Liu Yutao , Ma Haixia , Wang Shipeng , Niyitanga Evode , He Chunxia 
Published: March 2022

Fusarium graminearum is the main pathogen of Fusarium head blight (FHB), which causes huge economic losses every year. In this study, an attempt was made to control FHB from the point of view of the physiological behavior of the pathogen itself. Autophagic inhibitors and activators were used, and the pathogenicity-related indices of F. graminearum were measured. The results showed that under nitrogen-rich conditions, macroautophagy inhibition and activation greatly reduced the mycelium weight to 0.28 and 0.25 g/ml at 24 h, which were 17.82 and 24.77% lower than that of the control treatment, respectively. Mitophagy inhibition also significantly decreased the mycelium weight (P < 0.05). Conidial yield was found to be affected by factors related to autophagy occurrence. It was found that both autophagy inhibition and activation could reduce the conidiation of F. graminearum. The toxin contents in wheat medium of macroautophagy activation treatments were 0.678, 0.190, 0.402, and 0.195 μg/g when cultured for 8 and 24 h under 0% N and 100% N conditions, respectively, which were significantly higher than those of the control treatments (P < 0.05). The infection length was measured to characterize the infectivity of F. graminearum, and we found that the length was short under macroautophagy activation conditions. However, mitophagy did not seem to affect the infectivity of F. graminearum. In summary, the above results indicate that macroautophagy and mitophagy inhibition could reduce the pathogenicity of F. graminearum, which may provide a new perspective for management of plant fungal diseases.
Time-series monitoring of transgenic maize seedlings phenotyping exhibiting glyphosate tolerance
Authors: Tao Mingzhu , Feng Xuping , He Yong , Zhang Jinnuo , Bai Xiulin , Yang Guofeng , Wei Yuzhen 
Published: March 2022

AbstractDeveloping herbicide resistant cultivars is one of the effective methods to solve the safety problem caused by the use of herbicide. In this study, hyperspectral image was used to develop more robust leaf chlorophyll content (LCC) prediction model based on different datasets to finally analyze the response of LCC to glyphosate-stress. Chlorophyll a fluorescence (ChlF) was used to dynamically monitor the photosynthetic physiological response of transgenic glyphosate-resistant and wild glyphosate–sensitive maize seedlings, and applying chemometrics methods to extract time-series features to screen resistant cultivars. Both the proposed two transfer strategies achieved the best prediction of LCC with a coefficient of determination value of 0.84, and relative root mean square error of 4.03 for the prediction set. Based on the predicted LCC and ChlF data, we found the antioxidant system of glyphosate-sensitive plants is too fragile to protect themselves from the damage, while glyphosate-resistant plants could overcome it by activating more powerful antioxidant system. φE0, VJ, ψE0, and M0could be used to indicate damage caused by glyphosate to differentiate resistant cultivars. This study provided a new methodology to monitor LCC to finally analyze glyphosate tolerance in a time-series manner, and verified the feasibility of ChlF in crop breeding.HighlightThis study proposed a new methodology to monitor leaf chlorophyll content to finally analyze glyphosate tolerance in vivo, and verified the feasibility of chlorophyll a fluorescence in crop breeding.
A Novel Restraint Device to Improve Safety and Efficacy of Blood Collection During Non-Terminal Sampling of Bats
Authors: Morgan Clint N. , Mauldin Matthew R. , Jones Jeremy , Collier Brian , Nakazawa Yoshinori 
Published: March 2022

AbstractThere are a variety of blood collection techniques described in the literature for unanesthetized bats, which typically require multiple sharps (e.g., needles, lancets, etc.), competent animal handling for prolonged periods, and usually involve two individuals. With the challenges inherent to non-terminal sampling of blood from bats, as well as the growing need for the use of this technique across multiple disciplines and industries, an improved blood collection method is needed. We report the creation of a bat restraint device specifically designed for a single individual to safely collect blood from anesthetized or non-anesthetized bats. The utility of this restraint device is multifaceted, serving as a safety measure for both animal and handler, as well as increasing the efficiency of blood collection. The restraint device was tested during two laboratory bat studies, Afterwards, the users of the restraint device were provided with a 10-question survey questionnaire to record their opinions on its usage. In total 80% of responses were considered positive, 15% considered neutral, and 5% considered negative. Survey questions that all participants responded to positively when in comparison to the traditional method of blood collection from bats include “easier to perform”, “safer to bats”, and “safer to the individual”. While using the restraint devices during the laboratory studies, no needle sticks, bites, or scratches to laboratorians occurred, and no observable health issues or complication due to blood collection in the bats bled using the restraint devices.
Fewer non-native insects in freshwater than in terrestrial habitats across continents
Authors: Sendek Agnieszka , Baity-Jesi Marco , Altermatt Florian , Bader Martin K.-F. , Liebhold Andrew M. , Turner Rebecca , Roques Alain , Seebens Hanno , Spaak Piet , Vorburger Christoph , Brockerhoff Eckehard G. 
Published: March 2022

AbstractAimBiological invasions are a major threat to biodiversity in both aquatic and terrestrial habitats. Insects represent an important group of species in freshwater and terrestrial habitats, and they constitute a large proportion of non-native species. However, while many non-native insects are known from terrestrial ecosystems, it remains unclear how they are represented in freshwater habitats. Comparisons of the richness of invaders relative to the richness of native species between freshwater and terrestrial habitats are scarce, which hinders syntheses of invasion processes. Here, we used data from three regions on different continents to determine whether non-native insects are under- or overrepresented in freshwater compared to terrestrial assemblages.LocationEurope, North America, New ZealandMethodsWe compiled a comprehensive inventory of the native and non-native insect species established in freshwater and terrestrial habitats of the three study regions. We then contrasted the richness of non-native and native species among freshwater and terrestrial insects for all insect orders in each region. Using binomial regression, we analysed the proportions of non-native species in freshwater and terrestrial habitats across the three regions.ResultsIn most insect orders living in freshwater, non-native species were under-represented, while they were over-represented in a number of terrestrial orders. This pattern occurred in purely aquatic orders as well as in orders with both freshwater and terrestrial species. Overall, the proportion of non-native species was significantly lower in freshwater than in terrestrial species.Main conclusionsDespite the numerical and ecological importance of insects among all non-native species, non-native insect species are surprisingly rare in freshwater habitats, and this pattern is consistent across the three investigated study regions. We briefly review hypotheses concerning species traits and invasion pathways that are most likely to explain these patterns. Our findings contribute to a growing appreciation of drivers and impacts of biological invasions.
A cellular and molecular analysis of SoxB-driven neurogenesis in a cnidarian
Authors: Chrysostomou Eleni , Flici Hakima , Gornik Sebastian G , Salinas-Saavedra Miguel , Gahan James M , McMahon Emma T , Thompson Kerry , Hanley Shirley , Kilcoyne Michelle , Schnitzler Christine E. , Gonzalez Paul , Baxevanis Andreas D , Frank Uri 
Published: March 2022

ABSTRACTNeurogenesis is the generation of neurons from stem cells, a process that is regulated by SoxB transcription factors (TFs) in many animals. Although the roles of these TFs are well understood in bilaterians, how their neural function evolved is unclear. Here, we use Hydractinia symbiolongicarpus, a member of the early-branching phylum Cnidaria, to provide insight into this question. Using a combination of mRNA in situ hybridization, transgenesis, gene knockdown, transcriptomics, and in-vivo imaging, we provide a comprehensive molecular and cellular analysis of neurogenesis during embryogenesis, homeostasis, and regeneration in this animal. We show that SoxB genes act sequentially. Stem cells expressing Piwi1 and Soxb1, which have a broad developmental potential, become neural progenitors that express Soxb2 before differentiating into mature neural cells. Knockdown of SoxB genes resulted in complex defects in embryonic neurogenesis. Hydractinia neural cells differentiate while migrating from the aboral to the oral end of the animal, but it is unclear whether migration per se or exposure to different microenvironments is the main driver of their fate determination. Our data constitute a rich resource for studies aiming at addressing this question, which is at the heart of understanding neurological disorders in all animals, including humans.
Ontology-Aware Biomedical Relation Extraction
Authors: Aghaebrahimian Ahmad , Anisimova Maria , Gil Manuel 
Published: March 2022

MotivationAutomatically extracting relationships from biomedical texts among multiple sorts of entities is an essential task in biomedical natural language processing with numerous applications, such as drug development or repurposing, precision medicine, and other biomedical tasks requiring knowledge discovery. Current Relation Extraction (RE) systems mostly use one set of features, either as text, or more recently, as graph structures. The state-of-the-art systems often use resource-intensive hence slow algorithms and largely work for a particular type of relationship. However, a simple yet agile system that learns from different sets of features has the advantage of adaptability over different relationship types without an extra burden required for system re-design.ResultsWe model RE as a classification task and propose a new multi-channel deep neural network designed to process textual and graph structures in separate input channels. We extend a Recurrent Neural Network (RNN) with a Convolutional Neural Network (CNN) to process three sets of features, namely, tokens, types, and graphs. We demonstrate that entity type and ontology graph structure provide better representations than simple token-based representations for RE. We also experiment with various sources of knowledge, including data resources in the Unified Medical Language System (UMLS) to test our hypothesis. Extensive experiments on four well-studied biomedical benchmarks with different relationship types show that our system outperforms earlier ones. Thus, our system has state-of-the-art performance and allows processing millions of full-text scientific articles in a few days on one typical machine.