bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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&nbsp;
Authors: Gäckler Anja , Schönermarck Ulf , Dobronravov Vladimir , Manna Gaetano La , Denker Andrew , Liu Peng , Vinogradova Maria , Yoon Sung-Soo , Praga Manuel 
Published: December 2020

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.