Correction: The Influence of Human Connections and Collaboration on Research Grant Success at Various Career Stages: Regression Analysis.

[This corrects the article DOI: 10.2196/49905.].

The Influence of Human Connections and Collaboration on Research Grant Success at Various Career Stages: Regression Analysis.

BACKGROUND: Documenting the grant acquisition characteristics of a highly selective group of researchers could provide insights into the research and faculty development of talented individuals, and the insights gained to foster such researchers will help university management strengthen their research capacity. OBJECTIVE: This study examines the role of human connections in the success of biomedical researchers in Japanese universities. METHODS: This study used grant data from the Grants-in-Aid for Scientific Research (GIA) program, the largest competitive research funding program in Japan, to collect information on projects and their implementation systems obtained throughout the participants' careers. Grant success was measured by the number and amounts of the awards obtained while participants occupied the role of principal investigator. Human connections were quantified by the number of projects in which the participants took part as members and were classified by their relationship with the project leader. Data were matched with information on career history, publication performance, and experience of the participants with government-funded programs apart from GIA and were analyzed using univariate and multivariate regression analyses. RESULTS: Early-career interpersonal relationships, as measured using the h-index value of the researchers who provided the participants with their initial experience as project members, had a positive effect on grant success. The experience of contributing to prestigious research programs led by top researchers dramatically increased the cumulative amount of GIA awards received by the participants over time. Univariate logistic regression analyses revealed that more interactions with upper-level researchers resulted in fewer acquisitions of large programs (odds ratio [OR] 0.67, 95% CI 0.50-0.89). Collaboration with peers increased the success rate of ≥2 research grants in large programs in situations in which both the participant and project leader were professors (OR 1.16, 95% CI 1.06-1.26). Tracking the process of research development, we found that collaboration during the periods of 10 to 14 years and 15 to 19 years after completing a doctorate degree determined the size of the project that the participant would obtain-interactions with peer researchers and subordinates during the 10- to 14-year postdegree period had positive effects on ≥2 large-program acquisitions (OR 1.51, 95% CI 1.09-2.09 and OR 1.31, 95% CI 1.10-1.57, respectively), whereas interactions with subordinates during the 15- to 19-year postdegree period also had positive effects (OR 1.25, 95% CI 1.25-1.07). Furthermore, relationships that remained narrowly focused resulted in limited grant success for small programs. CONCLUSIONS: Human networking is important for improving an individual's ability to obtain external funding. The results emphasize the importance of having a high-h-indexed collaborator to obtain quality information early in one's career; working with diverse, nonsupervisory personnel at the midcareer stage; and engaging in synergistic collaborations upon establishing a research area in which one can take more initiatives.

Impact of supervisors' research style on young biomedical scientists' capacity development as measured by REDi, a novel index of crossdisciplinarity.

The challenge for medical schools in Japan is to develop research activities for innovation. This study aimed at analyzing the connection between the research output of "promising researchers" (next-generation leaders in terms of research activity) and their supervisors' past research activities to identify those factors that impact researchers' performance. Activity was analyzed from the viewpoints of productivity, coauthorship networks, and research impact using a novel index called the Research Diversity Index (REDi) that quantifies crossdisciplinarity. Research funding, which has not yet been fully utilized in correlation studies of the characteristics of authors, was also considered in this study. For the promising researchers extracted using betweenness centrality scores within coauthorship networks, there were diachronic correlations between the records of the promising researchers and those of their supervisors. Supervisor leadership as measured by the number of last-authored publications and extent of networking had a positive effect on the promising researchers productivity. Supervisors' research style of integrating knowledge from multiple fields, as measured by REDi, was negatively correlated with the publication impact of promising researchers, suggesting that REDi is useful as a novel indicator of research quality not being captured by existing indices. It was also noted that establishing an academic presence through extensive collaborations could be advantageous for obtaining research funding, especially from top-down government programs. The possible implications of this study for promoting research activities are the importance of incorporating new doctorates into research groups at an early stage and that of promoting interinstitutional, crossdisciplinary collaborations. Classification code: MSC: 62P10 Applications of statistics to biology and medical sciences; meta-analysis.JEL: Z1Z10 Cultural Economics • Economic Sociology • Economic Anthropology- General.

Influence of polymerization methods and priming agents on the bond strength between resin luting agents and gold alloy.

PURPOSE: To evaluate the influence of polymerization methods and a metal priming agent on the bond strength between gold alloy for metal ceramic restorations and dual-cure-type resin luting agents, and on the strength and hardness of the luting agents. METHODS: A total of 154 disks cast by a gold alloy were treated with or without a metal priming agent. One of the three luting agents was applied on the disk. The luting agent was either chemically or dual-polymerized. The shear bond strength was measured both before and after thermocycling. In addition, scanning electron microscope (SEM) observation, flexural strength test, and Knoop hardness test were performed. RESULTS: Significant differences among the luting agents were observed in terms of bond strength and flexural strength. Significant differences between chemically and dual-polymerized luting agents were observed regarding shear bond strength, flexural strength, and Knoop hardness before thermocycling. The application of the priming agent was effective only for a luting agent. CONCLUSION: Both bond strength and flexural strength differed among three luting agents. The effect of the priming agent on bond strength differed among the luting agents. Both the bond and flexural strength of a chemically polymerized luting agent differed before or after thermocycling.

An Optimized Protein Extraction Method for Gel-Free Proteomic Analysis of Opuntia Ficus-Indica.

Opuntia spp. is an economically important vegetable crop with high stress-tolerance and health benefits. However, proteomic analysis of the plant has been difficult due to the composition of its succulent cladodes; the abundant polysaccharides interfere with protein extraction. To facilitate proteomic analysis of this plant, we present a rapid and simple protein extraction method for Opuntia ficus-indica (L.) Miller. The optimized method produced highly reproducible protein patterns and was compatible with a gel-free quantitative workflow without the need for additional purification. We successfully analyzed the cladode mesocarp and exocarp tissues, resulting in the identification of 319 proteins. In addition, we used this method to examine the relative changes in the Opuntia proteome in response to salt stress to determine whether physiological changes could be captured. Qualified observations were obtained, revealing that salt stress increased phosphoenolpyruvate carboxylase abundance and decreased ribulose-bisphosphate carboxylase in young O. ficus-indica plants. These findings suggest that Crassulacean acid metabolism is promoted under salinity. This study highlights the efficacy of our optimized protein extraction method for elucidating the metabolic adaptations of Opuntia using gel-free proteomic analysis.

The Effect of Mung Bean (Vigna radiata (L.)) Coat Extract on Mouse Liver Metabolism During Progesterone Withdrawal.

Mung bean (Vigna radiata) is an immunomodulatory medicinal plant, which is recognized as a component of a traditional postpartum diet. The liver plays a crucial role in fatty acid synthesis under the control of various hormones that are affected by pregnancy. This study was designed to establish whether the mung bean water extract, which contains prostaglandins that can regulate corpus luteum maturation, provided any benefits to liver metabolism after the dynamic hormonal change associated with pregnancy. Female C57BL/6J mice were used, and all mice received daily injections of progesterone (5.0 mg/kg) for 5 days, after which progesterone was withdrawn for 3 days. Gel-free/label-free proteomic analysis revealed that the abundance of several proteins was affected in the liver. Hormone manipulation induced changes in lipid metabolism-related protein abundance; oral administration of mung bean coat extract (MBC) for 3 days mitigated the changes and downregulated the expression of Cpt1α, Akr1ß, and Srebp1 in the liver. Together with immunological leukocyte modulation assessed via proteomic analysis, we suggest that MBC may exert health-promoting effects through the modulation of lipid synthesis during postpartum recovery.

Female C57BL/6 and BALB/c mice differently use the acoustic features of male ultrasonic vocalizations for social preferences.

Male mice emit ultrasonic vocalizations (USVs) in response to the presence of female mice and their urine. Male USVs attract females, enhancing female reproductive functions, and are thus considered as the courtship song. Previous studies have shown that female mice exhibit disassortative social preferences for male USVs. However, it remains unclear what acoustic features female mice use for the development of these preferences. To address this, we examined social preferences of female C57BL/6 and BALB/c mice using the three-chamber preference test using recorded male USVs. To dissociate the peak frequencies of these USVs from their syllable structure, we digitally manipulated the peak frequencies accordingly. We found that female mice preferred USVs that were dissimilar to those of their own strain. We also observed that, while female C57BL/6 mice were sensitive to changes in the syllable structure and the peak frequency, female BALB/c mice were sensitive to differences in the syllable structure. Our results demonstrate that female C57BL/6 and BALB/c mice differently use the acoustic features such as the peak frequency and the syllable structure for exhibiting disassortative social preferences.

Subcellular Proteomics: Application to Elucidation of Flooding-Response Mechanisms in Soybean.

Soybean, which is rich in protein and oil, is cultivated in several climatic zones; however, its growth is markedly decreased by flooding. Proteomics is a useful tool for understanding the flooding-response mechanism in soybean. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and during stress. Under flooding, proteins related to signaling, stress and the antioxidative system are increased in the plasma membrane; scavenging enzymes for reactive-oxygen species are suppressed in the cell wall; protein translation is suppressed through inhibition of proteins related to preribosome biogenesis and mRNA processing in the nucleus; levels of proteins involved in the electron transport chain are reduced in the mitochondrion; and levels of proteins related to protein folding are decreased in the endoplasmic reticulum. This review discusses the advantages of a gel-free/label-free proteomic technique and methods of plant subcellular purification. It also summarizes cellular events in soybean under flooding and discusses future prospects for generation of flooding-tolerant soybean.

Effect of framework design on fracture load after thermal cycling and mechanical loading of implant-supported zirconia-based prostheses.

This study evaluated the effect of zirconia framework design on fracture load of implant-supported zirconia-based prostheses after thermal cycling and mechanical loading. Three different zirconia framework designs were investigated: uniform-thickness (UNI), anatomic (ANA), and supported anatomic (SUP) designs. Each framework was layered with feldspathic porcelain (ZAC group) or indirect composite material (ZIC group). The specimens then underwent fracture load testing after thermal cycling and cyclic loading. In the ZAC group, mean fracture load was significantly lower for UNI design specimens than for the other framework designs. In the ZIC group, there was no significant difference in mean fracture load between ANA design specimens and either UNI or SUP design specimens. To improve fracture resistance of implant-supported zirconia-based prostheses after artificial aging, uniformly thick layering material and appropriate lingual support with zirconia frameworks should be provided.

Proteomic Contributions to Medicinal Plant Research: From Plant Metabolism to Pharmacological Action.

Herbal medicine is a clinical practice of utilizing medicinal plant derivatives for therapeutic purposes. It has an enduring history worldwide and plays a significant role in the fight against various diseases. Herbal drug combinations often exhibit synergistic therapeutic action compared with single-constituent dosage, and can also enhance the cytotoxicity induced by chemotherapeutic drugs. To explore the mechanism underlying the pharmacological action of herbs, proteomic approaches have been applied to the physiology of medicinal plants and its effects on animals. This review article focuses on the existing proteomics-based medicinal plant research and discusses the following topics: (i) plant metabolic pathways that synthesize an array of bioactive compounds; (ii) pharmacological action of plants tested using in vivo and in vitro studies; and (iii) the application of proteomic approaches to indigenous plants with scarce sequence information. The accumulation of proteomic information in a biological or medicinal context may help in formulating the effective use of medicinal plants.

Metabolic profiles of flooding-tolerant mechanism in early-stage soybean responding to initial stress.

KEY MESSAGE: Metabolomic analysis of flooding-tolerant mutant and abscisic acid-treated soybeans suggests that accumulated fructose might play a role in initial flooding tolerance through regulation of hexokinase and phosphofructokinase. Soybean is sensitive to flooding stress, which markedly reduces plant growth. To explore the mechanism underlying initial-flooding tolerance in soybean, mass spectrometry-based metabolomic analysis was performed using flooding-tolerant mutant and abscisic-acid treated soybeans. Among the commonly-identified metabolites in both flooding-tolerant materials, metabolites involved in carbohydrate and organic acid displayed same profile at initial-flooding stress. Sugar metabolism was highlighted in both flooding-tolerant materials with the decreased and increased accumulation of sucrose and fructose, respectively, compared to flooded soybeans. Gene expression of hexokinase 1 was upregulated in flooded soybean; however, it was downregulated in both flooding-tolerant materials. Metabolites involved in carbohydrate/organic acid and proteins related to glycolysis/tricarboxylic acid cycle were integrated. Increased protein abundance of phosphofructokinase was identified in both flooding-tolerant materials, which was in agreement with its enzyme activity. Furthermore, sugar metabolism was pointed out as the tolerant-responsive process at initial-flooding stress with the integration of metabolomics, proteomics, and transcriptomics. Moreover, application of fructose declined the increased fresh weight of plant induced by flooding stress. These results suggest that fructose might be the critical metabolite through regulation of hexokinase and phosphofructokinase to confer initial-flooding stress in soybean.

Datasets of mung bean proteins and metabolites from four different cultivars.

Plants produce a wide array of nutrients that exert synergistic interaction among whole combinations of nutrients. Therefore comprehensive nutrient profiling is required to evaluate their nutritional/nutraceutical value and health promoting effect. In order to obtain such datasets for mung bean, which is known as a medicinal plant with heat alleviating effect, proteomic and metabolomic analyses were performed using four cultivars from China, Thailand, and Myanmar. In total, 449 proteins and 210 metabolic compounds were identified in seed coat; whereas 480 proteins and 217 metabolic compounds were detected in seed flesh, establishing the first comprehensive dataset of mung bean for nutraceutical evaluation.

Proteomic analysis of soybean seedling leaf under waterlogging stress in a time-dependent manner.

Leaf is sensitive to environmental changes and exhibits specific responses to abiotic stress. To identify the response mechanism in soybean leaf under waterlogging stress, a gel-free/label-free proteomic technique combined with polyethylene glycol fractionation was used. Attenuated photosynthesis by waterlogging stress in the leaf of soybean seedlings was indicated from proteomic results. Defensive mechanisms such as reactive oxygen species (ROS) scavenging was also recognized. Cluster analysis revealed that proteins that exhibit characteristic dynamics in response to waterlogging were mainly related to photosynthesis. Among the identified photorespiration-related proteins, the protein abundance and enzyme activity of hydroxypyruvate reductase were transiently increased in control plants, but were clearly decreased in response to waterlogging stress. These results suggest that waterlogging directly impairs photosynthesis and photorespiration. Furthermore, hydroxypyruvate reductase may be a critical enzyme controlling the rate of photorespiration.

Proteomics and metabolomics-driven pathway reconstruction of mung bean for nutraceutical evaluation.

Mung bean is a legume crop which has a various health-promoting effects. Although rich flavonoids are reported to be responsible for its biological activities, little is known about other nutrients that may potentiate the activities. To obtain information on mung bean nutritional properties, gel-free/label-free proteomic analysis and metabolomic profiling were combined. Pathway reconstruction detected that amino acid metabolism is more active in flesh. Coat contained wider variety of lipids and phenolic acids/flavonoids than flesh. Among the compounds detected in coat, sphingolipids, arachidonic acid, and prostaglandin E2 are compounds which are related to immune response induction. Furthermore, identification of prostaglandin F2α added scientific support to empirical validity of mung bean usage. The abundance of bioactive compounds such as naringenin, which can be metabolized into vitexin, varied among cultivars. These results suggest that lipids together with flavonoids might be potential responsible compounds for biological activity of mung bean coat and flesh.

Mung bean (Vigna radiata (L.)) coat extract modulates macrophage functions to enhance antigen presentation: A proteomic study.

The immunomodulatory effect of mung bean is mainly attributed to antioxidant properties of flavonoids; however, the precise machinery for biological effect on animal cells remains uncertain. To understand the physiological change produced by mung bean consumption, proteomic and metabolomic techniques were used. In vitro assay confirmed the importance of synergistic interaction among multiple flavonoids by IL-6 expression. Proteomic analysis detected that the abundance of 190 proteins was changed in lipopolysaccharide-stimulated RAW264.7 cells by treatment with coat extract. Pathway mapping revealed that a range of proteins were regulated including an interferon-responsive antiviral enzyme (2'-5'-oligoadenylate synthetase), antigen processing factors (immunoglobulin heavy chain-binding protein and protein disulfide-isomerase), and proteins related to proteasomal degradation. Major histocompatibility complex pathway was activated. These results suggest that mung bean consumption enhances immune response toward a Th2-promoting polarization. BIOLOGICAL SIGNIFICANCE: This study highlighted the immunomodulation of RAW264.7 cells in response to treatment with mung bean seed coat extract, using gel-free proteomic technique. The mechanism of immunomodulation by mung bean has not been described until today except for a report which identified HMGB1 suppression as a pathway underlying the protective effect against sepsis. This study suggested that the mung bean is involved in the regulation of antigen processing and presentation, and thus shifts immune response from acute febrile illness to specific/systemic and long-lasting immunity to protect the host.

Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress.

The efficiency of stress-induced adaptive responses of plants depends on intricate coordination of multiple signal transduction pathways that act coordinately or, in some cases, antagonistically. Protein post-translational modifications (PTMs) can regulate protein activity and localization as well as protein-protein interactions in numerous cellular processes, thus leading to elaborate regulation of plant responses to various external stimuli. Understanding responses of crop plants under field conditions is crucial to design novel stress-tolerant cultivars that maintain robust homeostasis even under extreme conditions. In this review, proteomic studies of PTMs in crops are summarized. Although the research on the roles of crop PTMs in regulating stress response mechanisms is still in its early stage, several novel insights have been retrieved so far. This review covers techniques for detection of PTMs in plants, representative PTMs in plants under abiotic stress, and how PTMs control functions of representative proteins. In addition, because PTMs under abiotic stresses are well described in soybeans under submergence, recent findings in PTMs of soybean proteins under flooding stress are introduced. This review provides information on advances in PTM study in relation to plant adaptations to abiotic stresses, underlining the importance of PTM study to ensure adequate agricultural production in the future.

Characterization of a novel flooding stress-responsive alcohol dehydrogenase expressed in soybean roots.

Alcohol dehydrogenase (Adh) is the key enzyme in alcohol fermentation. We analyzed Adh expression in order to clarify the role of Adh of soybeans (Glycine max) to flooding stress. Proteome analysis confirmed that expression of Adh is significantly upregulated in 4-day-old soybean seedlings subjected to 2 days of flooding. Southern hybridization analysis and soybean genome database search revealed that soybean has at least 6 Adh genes. The GmAdh2 gene that responded to flooding was isolated from soybean cultivar Enrei. Adh2 expression was markedly increased 6 h after flooding and decreased 24 h after floodwater drainage. In situ hybridization and Western blot indicated that flooding strongly induces Adh2 expression in RNA and protein levels in the root apical meristem. Osmotic, cold, or drought stress did not induce expression of Adh2. These results indicate that Adh2 is a flooding-response specific soybean gene expressed in root tissue.

Analyses of the proteomes of the leaf, hypocotyl, and root of young soybean seedlings.

The functions of organs in young soybean seedling were determined by means of proteomic analysis. Extracts from leaves, hypocotyls, and roots were separated by two-dimensional polyacrylamide gel electrophoresis, and the proteins were identified by mass spectrometry and protein sequencing. The identified proteins were categorized into various groups according to their function. The leaf was abundant in proteins associated with energy production (50.0%), the hypocotyl was rich in defense proteins (31.8%), and the root contained defense-related proteins (16.7%) and destination and storage proteins (26.7%). Stem 31-kDa glycoprotein, 20 kDa chaperonin, 50S ribosomal protein, and trypsin inhibitor were common to all three tissues. The sequence information obtained from the soybean proteome should be helpful in predicting the functions of unknown proteins.

Proteome analysis of early-stage soybean seedlings under flooding stress.

Proteomic analyses of soybean seedlings responding to flooding were conducted to identify proteins involved in such response. Soybean was germinated for 48 h and then subjected to flooding stress for 6-48 h. Proteomic analysis of hypocotyl and root was used in a time-dependent manner, and altered proteins were identified using soybean protein data file constructed for this research. Under flooding stress, 35 proteins were up-regulated, whereas 16 proteins were down-regulated at a 24-h time point. Changes in energy generation was recognized because several glycolytic enzymes were up-regulated. General stress response was also shown to occur as various reactive oxygen species scavengers were up-regulated. Other identified proteins with diverse functional categories suggest that flooding stress includes not only hypoxic stress, but also other stresses such as weak light, disease, and water stresses. In addition, proteins with unknown functions were shown to be positioned as hubs which activate other proteins in system response networks by protein-protein interaction analysis, suggesting that this type of interaction analysis is useful for screening of important factors in plant response to environmental stresses.

Soybean proteome database: a data resource for plant differential omics.

The Soybean Proteome Database aims to be a data repository for functional analyses of soybean responses to flooding injury, recognized as a major constraint for establishment and production of this plant. The current release contains 21 reference maps of soybean (Glycine max cv. Enrei) proteins electrophoresed on two-dimensional polyacrylamide gels of which the samples were collected from several organs, tissues and organelles. These reference maps include 7311 detected proteins and 532 identified proteins, or proteins for which a sequence or peptide peak has been determined. The database is searchable by protein properties such as accession number, description and isoelectric point and molecular weight range. The Soybean Proteome Database also integrates multiple "omes". An omics table reveals relationships among 106 mRNAs, 51 proteins and 89 metabolites that vary over time under flooding stress. The tabulated metabolites are anchored to a metabolome network. A unified temporal-profile tag attached to the mRNAs, proteins and metabolites facilitates retrieval of the data based on the temporal expression profiles. A graphical user interface based on dynamic HTML facilitates viewing the metabolome network as well as the profiles of multiple omes in a uniform manner. The entire database is available at http://proteome.dc.affrc.go.jp/Soybean/.