bluuebunny/crossref_metadata_2025 huggingface dataset:
Conceptualising, Operationalising, and Measuring Trust in Participatory Health Research Networks: a Scoping Review
Authors: Gilfoyle Meghan , MacFarlane Anne , Salsberg Jon
Published: December 2020

BackgroundThere are many described benefits of community-based participatory research (CBPR), such as increased relevance of research for those who must act on its findings. This has prompted researchers to better understand how CBPR functions to achieve these benefits through building sustainable research partnerships. Several studies have identified ‘trust’ as a key mechanism to achieve sustainable partnerships, which themselves constitute social networks. Although existing literature discuss trust and CBPR, or trust and social networks, preliminary searches reveal that none link all three concepts of trust, CBPR and social networks. Thus, we present our scoping review to systematically review and synthesize the literature exploring how trust is conceptualised, operationalised, and measured in CBPR and social networks.MethodsThis review follows guidelines from Levac et al, which follow the methodological framework of Arksey and O’Malley. We explored several electronic databases including Scopus, Medline, PubMed, Web of Science, CINAHL, Cochrane Library, Google Scholar, and PsychINFO. A search strategy was identified and agreed upon by the team in conjunction with a research librarian. Two independent reviewers screened articles by title and abstract, then by full-text based on pre-determined exclusion/inclusion criteria. A third reviewer arbitrated discrepancies regarding inclusions/exclusions. A thematic analysis was then conducted to identify relevant themes and sub-themes.Results Based on the 26 extracted references, several key themes and sub-themes were identified which highlighted the complexity and multidimensionality of trust as a concept. Our analysis revealed an additional emergent category that highlighted another important dimension of trust – outcomes pertaining to trust. Further, variation within how the studies conceptualised, operationalised, and measured trust was illuminated. Finally, the multidimensionality of trust provided important insight into how trust operates as a context, mechanism and outcome.ConclusionsFindings provide support for future research to incorporate trust as a lens to explore the social-relational aspects of partnerships and the scope to develop interventions to support trust in partnerships.
Genome-wide Identification, Expression, and Sequence Analysis of CONSTANT-like Gene Family in Cannabis Reveals Role in Plant Flowering Time Regulation
Authors: Pan Gen , Li Zheng , Yin Ming , Huang Siqi , Tao Jie , Chen Anguo , Li Jianjun , Tang Huijuan , Chang Li , Deng Yong , Li Defang , Zhao Lining
Published: December 2020

Background: Cannabis, an important industrial crop, has a high sensitivity to photoperiods. The flowering time of cannabis is one of its important agronomic traits, and has an important effect on its yield and quality. The CONSTANS-like (COL) gene plays a key role in the regulation of flowering in this plant. However, the specific biological and functional roles of the COL gene family in the cannabis is still unknown. Results: In this study, 13 CsCOL genes were identified in the cannabis genome. Phylogenetic analysis implied that the CsCOL proteins were divided into three subgroups, and each subgroups included conserved intron/exon structures and motifs. Chromosome distribution analysis showed that 13 CsCOL genes were unevenly distributed on 7 chromosomes, with chromosome 10 having the most CsCOL members. Colinearity analysis showed that two syntenic gene pairs of CsCOL4 and CsCOL11 were found in both rice and Gossypium raimondii. Among 13 CsCOLs, CsCOL6 and CsCOL12 were a pair of tandem duplicated genes, whereas CsCOL8 and CsCOL11 may have resulted from segmental duplication. Furthermore, tissue-specific expression showed that ten CsCOL genes were preferentially expressed in the leaves, one CsCOL in the stem, and two CsCOL in the female flower. Most CsCOL exhibited a diurnal oscillation pattern under different light treatment. Additionally, sequence analysis showed that CsCOL3 and CsCOL7 exhibited amino acid difference among the early-flowering cultivars and late flowering cultivars. Conclusion: This study provided insight into the potential functions studies of CsCOL genes, and highlight its roles in the regulation of flowering time in cannabis. Our results laid a foundation for the further elucidation of the functions of COLs in cannabis
First-principles calculation of atomic structure, stability and electronic structure of TaB2/SiC interface
Authors: Cheng Gong , Xiong Yuqing , Zhou Hui , He Yanchun , Zhang Kaifeng , Cao Shengzhu , Wang Keliang
Published: December 2020

The atomic structure, interface stability and electronic interaction of TaB2(0001)/SiC(111) interfaces were investigated by first principles study. The study found that the termination atom and stacking position are the key factors affecting the bonding strength and stability of the interface. On the basis of considering work of adhesion (Wad) and interfacial energy (γint), the Ta-TaB2/C-SiC centre-site stacked (Ta CS-C) and B-TaB2/C-SiC center-site stacked (B-CS-C) configurations were recognized as the most stable structures from ten different interface models. Electronic interaction of the two most stable interfaces were revealed by analyzing the charge density distribution, charge density difference and partial density of states (PDOS), and it was found that ionic and metallic bond coexisted in Ta CS-C interface, while covalent bond played a dominant role in B-CS-C interface.
Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across different sites
Authors: Shrestha Anish M.S. , Lilagan Crissa Ann I. , Guiao Joyce Emlyn B. , Romana-Eguia Maria Rowena R. , Lagman Ma. Carmen Ablan
Published: December 2020

Background: The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab seeds from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response.Results: We present the first ever transcriptome assembly of S. serrata obtained from a massive data set containing ~66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Based on sequence comparison to the fruitfly and shrimp proteomes, our assembly contains several thousands of almost full-length transcripts. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis of difference in heat response showed that between Cagayan and Bataan, there were 389 differently differentially expressed (DDE) genes associated with 48 signalling and stress-response pathways; and between Cagayan and Bicol, there were 101 DDE genes affecting 8 pathways.Conclusion: In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.
Extracellular vesicles released by the human gut symbiont Bacteroides thetaiotaomicron in the mouse intestine are enriched in a selected range of proteins that influence host cell physiology and metabolism
Authors: Stentz Regis , Wegmann Udo , Guirro Maria , Bryant Will , Ranjit Avani , Goldson Andrew J. , Brion Arlaine , Cross Kathryn , Booth Catherine , Miquel-Clopes Ariadna , Jones Emily , Gunning Patrick , Sudhakar Padhmanand , Módos Dezső , Brown Ian R. , Korcsmáros Tamás , Carding Simon R.
Published: December 2020

It is becoming increasingly clear that bacterial extracellular vesicles (BEVs) produced by members of the intestinal microbiota can contribute to microbe-host cell interactions that impact on host health. A major unresolved question is the nature of the cargo packaged into these BEVs and how they can impact on host cell function. Here we have analysed the proteome of BEVs produced by the major human gut symbiont Bacteroides thetaiotaomicron in both in vitro cultures using defined and complex medias, and in vivo in fed or fasted animals to determine the impact of nutrient stress on the BEV proteome, and to identify proteins specifically enriched in BEVs produced in vivo. In contrast to BEVs produced in vitro where limiting nutrient provision resulted in an increase in a large fraction of proteins, the protein content of BEVs extracted from fasted versus fed mice was less affected with similar numbers of proteins showing increased and decreased abundance. We identified 102 proteins exclusively enriched in BEVs in vivo of which the majority (66/102) were enriched independently of their expression in the parent cells implicating the existence of an active mechanism to drive the selection of a group of proteins for their secretion into BEVs within the intestine. Amongst these abundantly expressed proteins in BEVs in vivo were a bile salt hydrolase and a dipeptidyl peptidase IV that were characterised further and shown to be active and able to degrade host-derived substrates with defined roles in metabolism. Collectively these findings provide additional evidence for the role of BEVs in microbiota-host interactions with their contents playing key roles in the maintenance of intestinal homeostasis, and host metabolism.
Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening
Authors: Nilo-Poyanco Ricardo , Moraga Carol , Benedetto Gianfranco , Orellana Ariel , Almeida Andréa Miyasaka
Published: December 2020

Background Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening.Results To accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O’Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2,740 proteins, using the peach genome reference v1. After data pre-treatment, 1,663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively.Conclusions Shotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.
Efficacy and safety of the long-acting C5 inhibitor ravulizumab in patients with atypical hemolytic uremic syndrome triggered by pregnancy: a subgroup analysis 
Authors: Gäckler Anja , Schönermarck Ulf , Dobronravov Vladimir , Manna Gaetano La , Denker Andrew , Liu Peng , Vinogradova Maria , Yoon Sung-Soo , Praga Manuel
Published: December 2020

Background: Atypical hemolytic uremic syndrome (aHUS) triggered by pregnancy is a rare disease caused by dysregulation of the alternative complement pathway that occurs in approximately 1 in 25,000 pregnancies. The 311 phase 3 trial (NCT02949128) showed that ravulizumab, a long-acting C5 inhibitor obtained through selective modifications to eculizumab, is efficacious in inhibiting complement-mediated thrombotic microangiopathy (TMA) in patients with aHUS. In this analysis, we report outcomes in a subgroup of patients from the 311 study who developed TMA postpartum. Methods: This was a phase 3, multicenter trial evaluating efficacy and safety of ravulizumab in adults (≥18 years of age) with aHUS naïve to complement inhibitor treatment. The primary endpoint was complete TMA response (simultaneous platelet count normalization [≥150 x 109/L], lactate dehydrogenase normalization [≤246 U/L] and 25% improvement in serum creatinine) through the 183-day initial evaluation period. Additional efficacy endpoints included time to complete TMA response, hematologic normalization, and dialysis requirement status. Results: Eight patients presenting with TMA postpartum (median age of 37.7 [range; 22.1–45.2] years) were diagnosed with aHUS and received ≥1 dose of ravulizumab. Five patients (63%) were on dialysis at baseline. Complete TMA response was achieved in 7/8 patients (87.5%) in a median time of 31.5 days. Hematologic normalization was observed in all patients. All patients on dialysis at baseline discontinued dialysis within 21 days after treatment with ravulizumab. All patients showed continued improvements in the estimated glomerular filtration rate from baseline to Day 183. Three possible treatment-related adverse events were observed in 2 patients (arthralgia and nasopharyngitis [both non-severe]; urinary tract infection). No deaths or meningococcal infections occurred.Conclusions: Treatment with ravulizumab provided immediate and complete C5 inhibition, resulting in rapid clinical and laboratory improvements and complete TMA response through 183 days in patients with aHUS triggered by pregnancy. The safety profile observed in this subset of patients analysed is consistent with the 311 study investigating ravulizumab in patients with aHUS naïve to complement treatment.
Aesthetic evaluation of the labiolingual position of maxillary lateral incisors by orthodontists and laypersons
Authors: Jiang Xue , Cao Zhiwei , Yao Yang , Zhao Zhihe , Liao Wen
Published: December 2020

Background: The maxillary anterior teeth play a crucial role in smile aesthetics. Previous studies regarding the importance of maxillary lateral incisors for smile aesthetics concentrated on their size, incisor edge level, and inclination, etc. However, the aesthetic effect of lateral incisor movement in the spatial position has not been studied yet. Therefore, the purpose of this study was to explore the influence of the labiolingual position of maxillary lateral incisors on the aesthetic perception of smiles by orthodontists and laypersons, as well as analyze differences in this perception between male and female raters.Methods: A three-dimensional (3D) dental model was generated from the photograph of a man’s smile using iOrtho7.0 software (Time Angel, Wuxi, China). Based on this model, seven images were generated with different labiolingual positions of the maxillary lateral incisors in 0.5 mm increments (+ indicating labial translation, and - indicating lingual translation). The images were evaluated by 86 orthodontists and 161 laypersons using a visual analog scale, with lower scores indicating less attractiveness. Data were analyzed using Student’s t test and one-way analysis of variance with post hoc test.Results: There was no significant difference in smile ratings by males and females. Orthodontists assigned lower scores to all images than laypersons. The smile at +1.5 mm was considered the least attractive by orthodontists, while smiles at +1.5 mm and -1.5 mm were regarded as the least attractive by laypersons. The smile at 0 mm was evaluated as the most attractive by all raters. Laypersons gave different scores to smiles at 0 or -0.5 mm, but orthodontists did not.Conclusions: The labiolingual position of maxillary lateral incisors does affect the perception of smile aesthetics. Orthodontists may rate smile aesthetics more critically than laypersons. Therefore, communication and discussion between orthodontists and patients is needed to achieve better therapeutic and aesthetic outcomes.
Clinico-microbiological Profile of Burkholderia cepacia Keratitis: a Case Series
Authors: Ho Ming-Chih , Kang Eugene Yu-Chuan , Yeh Lung-Kun , Ma David HK , Lin Hsin-Chiung , Tan Hsin-Yuan , Chen Hung-Chi , Hsiao Ching-Hsi
Published: December 2020

Background: Burkholderia cepacia, an opportunistic pathogen mainly affecting patients with cystic fibrosis or immunocompromised, has rarely been documented as a cause of corneal infection. The clinical and microbiological profiles of B. cepacia keratitis are reported herein.Methods: We retrospectively reviewed the medical record of 17 patients with culture-proven B. cepacia keratitis, treated between 2000 and 2019 at Chang Gung Memorial Hospital, Taiwan. Our data included predisposing factors, clinical presentations, treatments, and visual outcomes of B. cepacia keratitis as well as the drug susceptibility of the causative agent.Results: The most common predisposing factor for B. cepacia keratitis was preexisting ocular disease (seven, 41.2 %), particularly herpetic keratitis (5). Polymicrobial infection was detected in seven (41.2 %) eyes. All B. cepacia isolates were susceptible to ceftazidime. Main medical treatments included levofloxacin or ceftazidime. Surgical treatment was required in five (29.4 %) patients. Only four (23.5 %) patients exhibited final visual acuity better than 20/200.Conclusions: B. cepacia keratitis primarily affects patients with preexisting ocular disease, particularly herpetic keratitis, and responds well to ceftazidime or fluoroquinolones. However, the visual outcomes are generally poor.
Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis
Authors: Dong Nan , Bandura Julia , Zhang Zhaolei , Wang Yan , Labadie Karine , Noel Benjamin , Davison Angus , Koene Joris M , Sun Hong-Shuo , Coutellec Marie-Agnes , Feng Zhong-Ping
Published: December 2020

Background. The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence information for the L. stagnalis CNS transcripts has been obtained from EST library and a de novo RNA-seq assembly, the quality of these assemblies is limited by a combination of low coverage of EST libraries, the fragmented nature of de novo assemblies, and lack of reference genome. Results. In this study, taking advantage of the recent availability of a preliminary L. stagnalis genome, we generated an RNA-seq library from the adult L. stagnalis CNS, using a combination of genome-guided and de novo assembly programs to identify 17,832 protein-coding L. stagnalis transcripts. We combined our library with existing resources to produce a transcript set with greater sequence length, completeness, and diversity than previously available ones. Using our assembly and functional domain analysis, we profiled L. stagnalis CNS transcripts encoding ion channels and ionotropic receptors, which are key proteins for CNS function, and compared their sequences to other vertebrate and invertebrate model organisms. Interestingly, L. stagnalis transcripts encoding numerous putative Ca2+ channels showed the most sequence similarity to those of Mus musculus, Danio rerio, Xenopus tropicalis, Drosophila melanogaster, and Caenorhabditis elegans, suggesting that many calcium channel-related signaling pathways may be evolutionarily conserved. Conclusions. Our study provides the most thorough characterization to date of the L. stagnalis transcriptome and provides insights into differences between vertebrates and invertebrates in CNS transcript diversity, according to function and protein class. Furthermore, this study provides a complete characterization of the ion channels of Lymnaea stagnalis, opening new avenues for future research on fundamental neurobiological processes in this model system.
Genome-wide in silico identification and expression analysis of beta-galactosidase family members in sweetpotato [Ipomoea batatas (L.) Lam.]
Authors: Hou Fuyun , Qin Zhen , Du Taifeng , Xu Tao , Li Aixian , Dong Shunxu , Ma Daifu , Wang Qingmei , Li Zongyun , Zhang Liming
Published: December 2020

Background: Sweetpotato (Ipomoea batatas (L.) Lam.) serves as an important food source for human beings. β-galactosidase (bgal) is a glycosyl hydrolase involved in cell wall modification, which plays essential roles in plant development and environmental stress adaptation. However, the function of bgal genes in sweetpotato remains unclear.Results: In this study, 17 β-galactosidase genes (Ibbgal) were identified in sweetpotato, which were classified into seven subfamilies using interspecific phylogenetic and comparative analyses. The promoter regions of Ibbgals harbored several stress, hormone and light responsive cis-acting elements. Quantitative real-time PCR results displayed that Ibbgal genes had the distinct expression patterns across different tissues and varieties. Moreover, the expression profiles under various hormonal treatments, abiotic and biotic stresses were highly divergent in leaves and root. Conclusions: Taken together, these findings suggested that Ibbgals might play an important role in plant development and stress responses, which provided evidences for further study of bgal function and sweetpotato breeding.
Genome sequencing and comparative genomic analysis of highly and weakly aggressive strains of Sclerotium rolfsii, the causal agent of peanut stem rot
Authors: Yan Liying , Wang Zhihui , Song Wanduo , Fan Pengmin , Lei Yong , Wan Liyun , Huai Dongxin , Chen Yuning , Wang Xin , Kang Yanping , Sudini Hari , Liao Boshou
Published: December 2020

Background: Stem rot caused by Sclerotium rolfsii is a very important soil-borne disease to peanut worldwide. S. rolfsii is a necrotrophic plant pathogenic fungus with an extensive host range and worldwide distribution. It can infect peanut stems, roots, pegs and pods, leading to varied yield losses. S. rolfsii strains GP3 and ZY collected from peanut in different provinces of China exhibited a significant difference in aggressiveness on peanut by artificial inoculation test. In this study, de-novo genome sequencing of these two distinct strains was performed aiming to reveal the genomic basis of difference in aggressiveness.Results: Scleotium rolfsii strains GP3 and ZY, with weak and high aggressiveness on peanut, exhibited similar growth rate and oxalic acid production in laboratory. The genomes of S. rolfsii strains GP3 and ZY were sequenced by Pacbio long read technology and exhibited 70.61 Mb and 70.51 Mb, with contigs of 27 and 23, and encoded 17,097 and 16,743 gene models, respectively. Comparative genomic analysis revealed that the pathogenicity-related gene repertoires, which might be associated with the aggressiveness, differed between GP3 and ZY. There were 58 and 45 unique pathogen-host interaction (PHI) genes in GP3 and ZY The ZY strain had more carbohydrate-active enzymes (CAZymes) in its secretome than GP3, especially in the glycoside hydrolase family (GH), the carbohydrate esterase family (CBM), and the polysaccharide lyase family (PL). GP3 and ZY also had different effector candidates and putative secondary metabolites synthetic gene clusters. These results indicated that differences in PHI, secreted CAZymes, effectors and secondary metabolites may play important roles in aggressive difference between these two strains.Conclusions: The data provided a further understanding of the S. rolfsii genome. Genomic comparison provided clues to the difference in aggressiveness of S. rolfsii strains.
Expression of Cyr61 is associated with Clinical Course in Patients with Crohn’s Disease
Authors: Lee Su-Mi , Lee Kyung-Hwa , Park Seon-Young , Chung Jin Ook , Kim Dong Hyun , Ju Jae Kyun , Lee Jae-Hyuk , Kim Hyun Soo
Published: December 2020

Backgrounds: Cysteine-rich angiogenic inducer 61 (Cyr61) is emerging as an important regulator of tissue homeostasis and wound repair. We aim to explore the colonic mucosal expression of Cyr61 and analyze the association between Cyr61 expression and clinical course in patients with Crohn’s disease (CD).Methods: Endoscopic samples were identified from 83 CD patients with and 372 controls without any pathologic findings by searching pathological reports. Among them, age- and sex- matched 43 of each group by a propensity score were selected to compare Cyr61 expression by immunohistochemistry (IHC). IHC scores for Cyr61 expression of CD patients were divided into tertiles to evaluate the association with clinical course. Results: The mean IHC scores for Cyr61 expression was higher in CD patients (86.5) than in controls (46.1, P<0.001). In CD patients, the mean IHC scores for Cyr61 expression (68.3) was lower in patients with clinical recurrence than in patients without recurrence (92.2, P=0.01). When CD patients were stratified into tertile groups according to IHC scores for Cyr61 expression, clinical recurrence rates tended to be lower in patients with high Cyr61 expression (P for trend=0.02). Compared with tertile 1 of Cyr61 expression, tertile 3 of Cyr 61 expression was associated with reduced risk of clinical recurrence (OR 0.43, 95%CI 0.20~0.92) after adjustment for age, sex and CD activity index at the time of colonoscopy in CD patients (P=0.03). Conclusions: Cyr61 mucosal expression in CD patients was inversely associated with clinical course. In the future, the possible therapeutic role of Cyr61 should be considered.
Long-period ground motion simulation using centroid moment tensor inversion solutions based on the regional three-dimensional model in the Kanto region, Japan
Authors: Takemura Shunsuke , Yoshimoto Kazuo , Shiomi Katsuhiko
Published: December 2020

We conducted centroid moment tensor (CMT) inversions of moderate (Mw 4.5–6.5) earthquakes in the Kanto region, Japan, using a local three-dimensional (3D) model. We then investigated the effects of our 3D CMT solutions on long-period ground motion simulations. Grid search CMT inversions were conducted using displacement seismograms for periods of 25–100 s. By comparing our 3D CMT solutions with those from the local one-dimensional (1D) catalog, we found that our 3D CMT inversion systematically provides magnitudes smaller than those in the 1D catalog. The Mw differences between 3D and 1D catalogs tend to be significant for earthquakes within the oceanic slab. By comparing ground motion simulations between 1D and 3D velocity models, we confirmed that observed Mw differences could be explained by differences in the rigidity structures around the source regions between 3D and 1D velocity models. The 3D velocity structures (especially oceanic crust and mantle) are important for estimating seismic moments in intraslab earthquakes, which are related to fault size estimation. A detailed discussion for intraslabe seismicity can be conducted by using the 3D CMT catalog. The seismic moments also directly affect the amplitudes of ground motions. The 3D CMT catalog allows us to directly conduct the precise forward and inverse modeling of long-period ground motion without adjusting source models, which have been typically applied in the cases using the 1D CMT catalog. We also conducted long-period ground motion simulations using our 3D CMT solutions to evaluate the reproducibility of long-period ground motions at stations within the Kanto Basin. The simulations of our 3D CMT solutions well-reproduced observed ground motions for periods longer than 10 s, even at stations within the Kanto Basin. The reproducibility of simulations was improved from those using solutions in the 1D catalog.
Numerical prediction of sporadic E layer occurrence using GAIA
Authors: Shinagawa Hiroyuki , Tao Chihiro , Jin Hidekatsu , Miyoshi Yasunobu , Fujiwara Hitoshi
Published: December 2020

A sporadic E layer has significant influence on radio communications and broadcasting, and predicting the occurrence of sporadic E layers is one of the most important issues in space weather forecast. While sporadic E layer occurrence and the magnitude of the critical sporadic E frequency ( foEs ) have clear seasonal variations, significant day-to-day variations as well as regional and temporal variations also occur. Because of the highly complex behavior of sporadic E layers, the prediction of sporadic E layer occurrence has been one of the most difficult issues in space weather forecast. To explore the possibility of numerically predicting sporadic E layer occurrence, we employed the whole atmosphere–ionosphere coupled model GAIA, examining parameters related to the formation of sporadic E layer such as vertical ions velocities and vertical ion convergences at different altitudes between 90 km and 150 km. By comparing those parameters in GAIA with observed foEs data obtained by ionosonde observations in Japan, we found that variations in the vertical ion convergence at 120 km altitude agree fairly well with variations in foEs . This result suggests that sporadic E layer occurrence can be numerically predicted using the parameters derived from GAIA. We have recently developed a real-time GAIA simulation system that can predict atmosphere–ionosphere conditions for a few days ahead. We present an experimental prediction scheme and a preliminary result for predicting sporadic E layer occurrence.
Study on Suitable Analysis Method for HIV-1 Non-catalytic Integrase Inhibitor
Authors: Park Ki Hoon , Kim Minjee , Bae Seoung Eun , Lee Hee Jung , Kim Kyung-Chang , Choi Byeong Sun , Kim Young Bong
Published: December 2020

Background: Integrase (IN) is an essential protein for HIV replication that catalyzes insertion of the reverse-transcribed viral genome into the host chromosome during the early steps of viral infection. Highly active anti-retroviral therapy (HAART) is a HIV/AIDS treatment method that combines three or more antiviral drugs often formulated from compounds that inhibit the activities of viral reverse transcriptase and protease enzymes. Early IN inhibitors (INIs) mainly serve as integrase strand transfer inhibitors (INSTI) that disrupt strand transfer by binding the catalytic core domain (CCD) of IN. However, mutations of IN can confer resistance to INSTI. Therefore, non-catalytic integrase inhibitors (NCINI) have been developed as next-generation INIs. Methods: In this study, we evaluated and compared the activity of INSTI and NCINI according to the analysis method. Antiviral activity was compared using p24 ELISA with MT2 cell and TZM-bl luciferase system with TZM-bl cell. Each drug was serially diluted and treated to MT2 and TZM-b1 cells, infected with HIV-1 AD8 strain and incubated for 5 and 2 days, respectively. Additionally, to analyze properties of INSTI and NCINI, transfer inhibition assay and 3'-processing inhibition assay were performed. Results: During screening of INIs using the p24 ELISA and TZM-bl luciferase systems, we found an inconsistent result with INSTI and NCINI drugs. Following infection of MT2 and TZM-bl cells with T-tropic HIV-1 strain, both INSTI and NCINI treatments induced significant p24 reduction in MT2 cells. However, NCINI showed no antiviral activity in the TZM-bl luciferase system, indicating that this widely used and convenient antiretroviral assay is not suitable for screening of NCINI compounds that target the second round of HIV-1 replication. Conclusion: Accordingly, we recommend application of other assay procedures, such as p24 ELISA or reverse transcription activity, in lieu of the TZM-bl luciferase system for preliminary NCINI drug screening. Utilization of appropriate analytical methods based on underlying mechanisms is necessary for accurate assessment of drug efficacy.
It’s a woman’s thing: Gender roles sustaining the practice of female genital mutilation among the Kassena-Nankana of northern Ghana
Authors: AKWEONGO PATRICIA , Jackson Elizabeth F. , Appiah-Yeboah Shirley Afua , Sakeah Evelyn , Phillips James F.
Published: December 2020

The practice of female genital mutilation (FGM) in traditional African societies is grounded in traditions of patriarchy that subjugate women. It is widely assumed that approaches to eradicating the practice must therefore focus on women’s empowerment and changing gender roles. MethodsThis paper presents findings from a qualitative study of the FGM beliefs and opinions of men and women in Kassena-Nankana District of northern Ghana. Data are analyzed from twenty-two focus group panels of young women, young men, reproductive age women, and male social leaders. ResultsThe social systemic influences on FGM decision-making are complex. Men represent exogenous sources of social influence on FGM decisions through their gender roles in the patriarchal system. As such, their FGM decision influence is more prominent for uncircumcised brides at the time of marriage than for FGM decisions concerning unmarried adolescents. Women in extended family compounds are relatively prominent as immediate sources of influence on FGM decision-making for both brides and adolescents. Circumcised women are the main source of social support for the practice, which they exercise through peer pressure in concert with co-wives. Junior wives entering a polygynous marriage or a large extended family are particularly vulnerable to this pressure. Men are less influential and more open to suggestions of eliminating the practice of FGM than women. ConclusionFindings attest to the need for social research on ways to involve men in the promotion of FGM abandonment, building on their apparent openness to social change. Investigation is also needed on ways to marshal women’s social networks for offsetting their extended family familial roles in sustaining FGM practices.
miR-335-5p suppresses gastric cancer progression by targeting MAPK10
Authors: Gao Yi , Wang Yanfeng , Wang Xiaofei , Zhao Changan , Wang Fenghui , Du Juan , Zhang Huahua , Shi Haiyan , Feng Yun , Li Dan , Yan Jing , Yao Yan , Hu Weihong , Ding Ruxin , Zhang Mengjie , Wang Lumin , Huang Chen , Zhang Jing
Published: December 2020

Background: Recent studies have established the roles of microRNAs (miRNAs) in cancer progression. The aberrant expression of miR-335-5p has been reported in many cancers, including gastric cancer (GC). In this study, the precise roles of miR-335-5p in GC as well as the molecular mechanisms underlying its effects, including the role of its target MAPK10, were evaluated.Methods: Quantitative real-time PCR was used to evaluate miR-335-5p levels in GC cell lines and tissues. MTT and colony formation assays were used to detect cell proliferation, and Transwell and wound-healing assays were used to evaluate the invasion and migration of GC cells. The correlation between levels of miR-335-5p and the cell cycle-related target gene mitogen-activated protein kinase 10 (MAPK10) in GC was analyzed. In addition, the candidate target was evaluated by a luciferase reporter assay, qRT-PCR, and western blotting.Results: The levels of miR-335-5p were downregulated in GC tissues and cell lines. Furthermore, miR-335-5p inhibited the proliferation and migration of GC cells and induced apoptosis. Additionally, miR-335-5p arrested the cell cycle at the G1/S phase in GC cells in vitro. Levels of miR-335-5p and the cell cycle-related target gene MAPK10 in GC were correlated, and MAPK10 was directly targeted by miR-335-5p.Conclusions: These data suggest that miR-335-5p is a tumor suppressor and acts via MAPK10 to inhibit GC progression.
Evaluation of the Solar Quiet Reference Field (SQRF) Model for Space Weather Applications in the South America Magnetic Anomaly
Authors: Chen Sony Su , Denardini Clezio Marcos , Resende Láysa C. A. , Chagas Ronan A. J. , Moro Juliano , Silva Régia P. , Carmo Carolina S. , Picanço Giorgio A. S.
Published: December 2020

In the present work, we evaluate the accuracy of the Solar Quiet Reference Field (SQRF) model for estimating and predicting the geomagnetic solar quiet (Sq) daily field variation in the South America Magnetic Anomaly (SAMA) region. This model is based on the data set of fluxgate magnetometers from 12 magnetic stations of the Embrace Magnetometer Network (Embrace MagNet) from 2010 to 2018. The model predicts the monthly average horizontal field of the geomagnetic quiet (Sq-H) daily variation solving a set of equations for the specified geographic coordinates in terms of the solar cycle activity, the day of the year, and the universal time. We carried out two comparisons between the prediction and observational data of the Sq-H field. The first part attempts to evaluate the accuracy for estimating the Sq-H field over Medianeira (25.30°S, 54.11°W, dip angle: -33.45°) by using linear interpolation on the SQRF coefficients. The second part of the analysis attempts to evaluate the accuracy for predicting the quiet daily field variation over Cachoeira Paulista (22.70°S, 45.01°W, dip angle: -38.48°). The results of the prediction for both locations show that this empirical model presents a good agreement with the Sq-H field obtained from the magnetic field data. The accuracy of the SQRF model (high correlation, r >0.9) provides a high potential for estimating and predicting geomagnetic quiet daily field variation for space weather applications.
Chloroplast Genome Variation and Phylogenetic Relationships of Atractylodes species
Authors: wang yiheng , Wang Sheng , Liu Yanlei , Yuan Qingjun , Sun Jiahui , Guo Lanping
Published: December 2020

Background：Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing.Results: The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42-47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions: Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.
Qigong mind-body program for caregivers of cancer patients: Design of a pilot three-arm randomized clinical trial
Authors: Shani Pinky , Raeesi Kristin , Walter Eli , Lewis Kai , Wang Wanyi , Cohen Lorenzo , Yeh Gloria Y , Lengacher Cecile A. , Wayne Peter M.
Published: December 2020

Background: Informal caregivers, often family and friends, experience significant psychological and physical distress leading to reductions in health and quality of life (QOL). Mind-body interventions focused on caregivers are often limited and do not address multiple barriers, including caregivers’ economic, geographic, and time constraints. Translation of in-person, community-based interventions to internet-based delivery may offer greater accessibility for caregivers, leading to increased adherence. Methods: Caring for Caregivers with Mind-Body Exercise implements a three-arm, pilot, randomized controlled trial to evaluate the feasibility of delivering a Qigong intervention (Eight Brocades) to cancer caregivers. A total of 54 cancer caregivers will be randomized into one of three 12-week programs: (1) community-based Qigong; (2) internet-based Qigong; or (3) a self-care control group. Study specific aims include 1) Modify intervention content for online delivery; 2) Evaluate the feasibility of recruiting and retaining cancer caregivers into a 12-week clinical trial; and 3) Evaluate the feasibility of collecting and managing data, and the suitability of questionnaires for this population. Several outcomes will be assessed, including caregiver QOL, caregiver burden, caregiver distress, perceived social support, physical function, and cognitive function. A 6-month follow-up will also assess longer-term changes in QOL and psychosocial wellbeing.Discussion: Findings will be used to inform the design and conduct of a large-scale comparative effectiveness trial evaluating caregivers who received Qigong training delivered through community-based vs internet-based programs. A finding that either or both programs are effective would inform care and options for caregivers.Trial registration: NCT04019301; registered on July 15, 2019; clinicaltrials.gov.
Overcoming Bioprocess Bottlenecks in the Large-Scale Expansion of High Quality hiPSC Aggregates in Vertical-Wheel Stirred Suspension Bioreactors
Authors: Borys Breanna S , Dang Tiffany , So Tania , Rohani Leili , Revay Tamas , Walsh Tylor , Thompson Madalynn , Argiropoulos Bob , Rancourt Derrick E. , Jung Sunghoon , Hashimura Yas , Lee Brian , Kallos Michael S.
Published: December 2020

BackgroundHuman induced pluripotent stem cells (hiPSCs) hold enormous promise in accelerating breakthroughs in understanding human development, drug screening, disease modeling and cell and gene therapies. Their potential, however, has been bottlenecked in a mostly laboratory setting due to bioprocess challenges in the scale-up of large quantities of high-quality cells for clinical and manufacturing purposes. While several studies have investigated the production of hiPSCs in bioreactors, the use of conventional horizontal-impeller, paddle and rocking-wave mixing mechanisms have demonstrated unfavourable hydrodynamic environments for hiPSC growth and quality maintenance. This study focused on using computational fluid dynamics (CFD) modeling to aid in characterizing and optimizing the use of vertical-wheel bioreactors for hiPSC production.MethodsThe vertical-wheel bioreactor was modeled with CFD simulation software Fluent at agitation rates between 20rpm and 100rpm. These models produced fluid flow patterns that mapped out a hydrodynamic environment to guide in the development of hiPSC inoculation and in-vessel aggregate dissociation protocols. The effect of single-cell inoculation on aggregate formation and growth was tested at select CFD modeled agitation rates and feeding regimes in the vertical-wheel bioreactor. An in-vessel dissociation protocol was developed through the testing of various proteolytic enzymes and agitation exposure times.ResultsCFD modeling demonstrated the unique flow pattern and homogeneous distribution of hydrodynamic forces produced in the vertical-wheel bioreactor, making it the opportune environment for systematic bioprocess optimization of hiPSC expansion. We developed a scalable, single-cell inoculation protocol for the culture of hiPSCs as aggregates in vertical-wheel bioreactors, achieving over 30-fold expansion in 6 days without sacrificing cell quality. We have also provided the first published protocol for in-vessel hiPSC aggregate dissociation, permitting the entire bioreactor volume to be harvested into single-cells for serial passaging into larger scale reactors. Importantly, the cells harvested and re-inoculated into scaled-up vertical-wheel bioreactors not only maintained consistent growth kinetics, they maintained a normal karyotype and pluripotent characterization and function.ConclusionsTaken together, these protocols provide a feasible solution for the culture of high quality hiPSCs at a clinical and manufacturing scale by overcoming some of the major documented bioprocess bottlenecks.
Salting-Out Induced Liquid-Liquid Microextraction for Alogliptin Benzoate Determination in Human Plasma by HPLC/UV
Authors: Hammad Sherin Farouk , Abdallah Inas , Bedair Alaa , Mansour Fotouh
Published: December 2020

Salting-out induced liquid-liquid microextraction method has been developed for plasma sample treatment before determination of alogliptin by high performance liquid chromatography with UV detection. Several parameters were optimized to achieve maximum enrichment, including type of extractant, volume of extractant, type of anion, type of cation, salt amount and pH. The optimum conditions were attained using 500 µL of acetonitrile, added to 1 mL of aqueous sample containing 250 mg of sodium chloride at pH 12. An RP-HPLC method was developed and validated according to the International Conference on Harmonization guidelines M10. The method was linear in the concentration range of 0.1 to 50 µg/mL (correlation coefficient= 0.997). The limit of detection was 0.019 µg/mL and limit of quantitation was 0.06 µg/mL. The method was accurate and precise with an average % recovery of 99.7% and a % relative standard deviation ranging between 1.5 and 2.5. These results showed that the salting-out induced liquid-liquid microextraction methods could be better than other sample preparation protocols in terms of sensitivity, easiness, solvent consumption and waste reduction.