bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between flower stalk elongation, anArabidopsisdevelopmental trait, and the subcellular location and movement dynamics of the nonstructural protein P3 ofTurnip mosaic virus
Authors: López‐González Silvia , Navarro José Antonio , Pacios Luis F. , Sardaru Papaiah , Pallás Vicente , Sánchez Flora , Ponz Fernando 
Published: August 2020

AbstractVirus infections affect plant developmental traits but this aspect of the interaction has not been extensively studied so far. Two strains ofTurnip mosaic virusdifferentially affectArabidopsisdevelopment, especially flower stalk elongation, which allowed phenotypical, cellular, and molecular characterization of the viral determinant, the P3 protein. Transiently expressed wild‐type green fluorescent protein‐tagged P3 proteins of both strains and selected mutants of them revealed important differences in their behaviour as endoplasmic reticulum (ER)‐associated peripheral proteins flowing along the reticulum, forming punctate accumulations. Three‐dimensional (3D) model structures of all expressed P3 proteins were computationally constructed through I‐TASSER protein structure predictions, which were used to compute protein surfaces and map electrostatic potentials to characterize the effect of amino acid changes on features related to protein interactions and to phenotypical and subcellular results. The amino acid at position 279 was the main determinant affecting stalk development. It also determined the speed of ER‐flow of the expressed proteins and their final location. A marked change in the protein surface electrostatic potential correlated with changes in subcellular location. One single amino acid in the P3 viral protein determines all the analysed differential characteristics between strains differentially affecting flower stalk development. A model proposing a role of the protein in the intracellular movement of the viral replication complex, in association with the viral 6K2 protein, is proposed. The type of association between both viral proteins could differ between the strains.
Breakthrough invasive fungal infections: Who is at risk?
Authors: Jenks Jeffrey D. , Cornely Oliver A. , Chen Sharon C.‐A. , Thompson George R. , Hoenigl Martin 
Published: August 2020

AbstractThe epidemiology of invasive fungal infections (IFIs) in immunocompromised individuals has changed over the last few decades, partially due to the increased use of antifungal agents to prevent IFIs. Although this strategy has resulted in an overall reduction in IFIs, a subset of patients develop breakthrough IFIs with substantial morbidity and mortality in this population. Here, we review the most significant risk factors for breakthrough IFIs in haematology patients, solid organ transplant recipients, and patients in the intensive care unit, focusing particularly on host factors, and highlight areas that require future investigation.
OsFD4 promotes the rice floral transition via florigen activation complex formation in the shoot apical meristem
Authors: Cerise Martina , Giaume Francesca , Galli Mary , Khahani Bahman , Lucas Jérémy , Podico Federico , Tavakol Elahe , Parcy François , Gallavotti Andrea , Brambilla Vittoria , Fornara Fabio 
Published: August 2020

Summary

In rice, the florigens Heading Date 3a (Hd3a) and Rice Flowering Locus T 1 (RFT1), OsFD‐like basic leucine zipper (bZIP) transcription factors, and Gf14 proteins assemble into florigen activation/repressor complexes (FACs/FRCs), which regulate transition to flowering in leaves and apical meristem. Only OsFD1 has been described as part of complexes promoting flowering at the meristem, and little is known about the role of other bZIP transcription factors, the combinatorial complexity of FAC formation, and their DNA‐binding properties.

Here, we used mutant analysis, protein–protein interaction assays and DNA affinity purification (DAP) sequencing coupled to in silico prediction of binding syntaxes to study several bZIP proteins that assemble into FACs or FRCs.

We identified OsFD4 as a component of a FAC promoting flowering at the shoot apical meristem, downstream of OsFD1. The osfd4 mutants are late flowering and delay expression of genes promoting inflorescence development. Protein–protein interactions indicate an extensive network of contacts between several bZIPs and Gf14 proteins. Finally, we identified genomic regions bound by bZIPs with promotive and repressive effects on flowering.

We conclude that distinct bZIPs orchestrate floral induction at the meristem and that FAC formation is largely combinatorial. While binding to the same consensus motif, their DNA‐binding syntax is different, suggesting discriminatory functions.
The FUSED LEAVES1‐ADHERENT1 regulatory module is required for maize cuticle development and organ separation
Authors: Liu Xue , Bourgault Richard , Galli Mary , Strable Josh , Chen Zongliang , Feng Fan , Dong Jiaqiang , Molina Isabel , Gallavotti Andrea 
Published: August 2020

Summary

All aerial epidermal cells in land plants are covered by the cuticle, an extracellular hydrophobic layer that provides protection against abiotic and biotic stresses and prevents organ fusion during development.

Genetic and morphological analysis of the classic maize adherent1 (ad1) mutant was combined with genome‐wide binding analysis of the maize MYB transcription factor FUSED LEAVES1 (FDL1), coupled with transcriptional profiling of fdl1 mutants.

We show that AD1 encodes an epidermally‐expressed 3‐KETOACYL‐CoA SYNTHASE (KCS) belonging to a functionally uncharacterized clade of KCS enzymes involved in cuticular wax biosynthesis. Wax analysis in ad1 mutants indicates that AD1 functions in the formation of very‐long‐chain wax components. We demonstrate that FDL1 directly binds to CCAACC core motifs present in AD1 regulatory regions to activate its expression. Over 2000 additional target genes of FDL1, including many involved in cuticle formation, drought response and cell wall organization, were also identified.

Our results identify a regulatory module of cuticle biosynthesis in maize that is conserved across monocots and eudicots, and highlight previously undescribed factors in lipid metabolism, transport and signaling that coordinate organ development and cuticle formation.
Screening for prevalence and abundance of Capnocytophaga spp by analyzing NGS data: A scoping review
Authors: Jolivet‐Gougeon Anne , Bonnaure‐Mallet Martine 
Published: August 2020

AbstractBackgroundCapnocytophaga spp. are commensal bacteria of the oral cavity and constitute a genus of the core microbiome.ObjectiveThis genus is responsible for many local and systemic conditions in both the immunocompetent and immunocompromised patients, but its beneficial or deleterious role in the microbiota has been little explored.DesignOnline databases were used to identify papers published from 1999 to 2019 based on next‐generation sequencing (NGS) data to study comparative trials. Work using other identification methods, case reports, reviews, and non‐comparative clinical trials was excluded.Results and conclusionWe selected 42 papers from among 668 publications. They showed a link between the abundance of Capnocytophaga spp. in the oral microbiota and various local pathologies (higher for gingivitis and halitosis; lower in active smokers, etc.) or systemic diseases (higher for cancer and carcinomas, IgA nephropathy, etc.). After discussing the limits inherent to the NGS techniques, we present several technical and biological hypotheses to explain the diversity of results observed between studies, as well as the links between the higher or lower abundance of Capnocytophaga spp and the appearance of local or systemic conditions and diseases.
Salvage surgery in head and neck cancer
Authors: van Weert Stijn , Leemans C. René 
Published: August 2020

AbstractSalvage surgery after failed organ preservation treatment offers challenges for both the patient and the surgeon. The outcome is often uncertain and even today, 5‐year overall survival does not exceed 50 per cent. The chemoradiotherapy induced toxicity asks for meticulous discussion and planning in a multidisciplinary manner in a changing environment of increasing incidence of human papillomavirus induced oropharyngeal tumours, evolving surgical techniques and patient participation. Herein, we discuss the latest literature on salvage surgery and the need for identifying the proper prognosticators to ensure for an optimal treatment plan in potentially salvageable patients.
Adult congenital heart disease and anesthesia: An educational review
Authors: Lei Lei Emma , Heggie Jane 
Published: August 2020

AbstractPrognosis has dramatically improved among children with congenital heart disease (CHD), and the median survival for severe CHD is currently 25 years (ie, into adulthood). However, additional cardiac surgeries are often necessary in adults with CHD, whose unique cardiovascular anatomy and physiology necessitate specialized management by experts in adult CHD (ACHD) during the perioperative period. ACHD is characterized by a combination of congenital cardiac lesions, intervention‐related anomalies that have developed over time, comorbidities caused by long‐standing CHD, and comorbidities related to various syndromes and lifestyle factors. The present educational review discusses the transition from pediatric to adult cardiac care, comorbidities that develop as a result of ACHD, the assessments necessary for patients with ACHD prior to both cardiac and noncardiac surgeries, and the key ACHD lesions relevant to perioperative management.
Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
Authors: Chawla Harmeet Singh , Lee HueyTyng , Gabur Iulian , Vollrath Paul , Tamilselvan‐Nattar‐Amutha Suriya , Obermeier Christian , Schiessl Sarah V. , Song Jia‐Ming , Liu Kede , Guo Liang , Parkin Isobel A. P. , Snowdon Rod J. 
Published: August 2020

SummaryGenome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single‐nucleotide polymorphism (SNP). In recent years, there have been a number of studies associating large chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloguing small‐ (30–10 000 bp) to mid‐scale (10 000–30 000 bp) SV and their impact on evolution and adaptation‐related traits in plants. This might be attributed to complex and highly duplicated nature of plant genomes, which makes them difficult to assess using high‐throughput genome screening methods. Here, we describe how long‐read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small‐ to mid‐scale SV in a major allopolyploid crop species, Brassica napus. We found that up to 10% of all genes were affected by small‐ to mid‐scale SV events. Nearly half of these SV events ranged between 100 bp and 1000 bp, which makes them challenging to detect using short‐read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco‐geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium‐coverage long‐read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.
Development and Validation of the Japanese Version of Quality of Life Assessment of Spina Bifida in Children (QUALAS‐C‐J)
Authors: Kawahara Tae , Sugita Yoshifumi , Momose Hitoshi , Szymanski Konrad M. , Hida Eisuke , Yamazaki Akemi 
Published: August 2020

AbstractBackgroundWe previously developed the Japanese version of The Quality of Life Assessment of Spina Bifida in Teenagers, a health‐related quality‐of‐life instrument specific to children aged 13–17 years with spina bifida (SB). The Quality of Life Assessment of Spina Bifida in Children is a version of this questionnaire for children aged 8–12 years. The purpose of this study was to develop a Japanese version of the Quality of Life Assessment of Spina Bifida in Children (QUALAS‐C‐J) and verify its reliability and validity.MethodsThree urologists specializing in SB, 2 nurses, and 1 statistician developed the QUALAS‐C‐J and conducted a pilot and main survey. Participants included children with SB and non‐disabled (ND) children. Participants completed the QUALAS‐C‐J and the Japanese version of KIDSCREEN‐27 (J‐KIDSCREEN) without parental help.ResultsFive children with SB participated in the pilot study and provided face and content validity. Sixty‐three children with SB and 40 age‐ and sex‐matched ND children participated in the main survey. The intraclass correlation coefficient in the retest was 0.80, and Cronbach's alpha in each domain was 0.73. The validity was verified by factor analysis, convergent / divergent validity, and known‐groups validity. Factor analysis converged to the same two‐factor structure as the original version. The correlation between QUALAS‐C‐J and J‐KIDSCREEN‐27 was weak (r=−0.06‐0.30). The scores of both groups for the two domains of the QUALAS‐C‐J were significantly lower in SB than ND children.ConclusionsQUALAS‐C‐J is easy to answer, suitable for Japanese children with SB, reliable, and valid. It can be a communication tool for children with SB, medical staff, families, communities, and school teachers.
The effects of nutritional status and intervention on pulmonary functions in pediatric cystic fibrosis patients
Authors: Kilinc Ayse Ayzit , Beser Omer Faruk , Ugur Ebru Pelin , Cokugras Fugen Cullu , Cokugras Haluk 
Published: August 2020

AbstractBackgroundCystic fibrosis (CF) causes malabsorption of nutrients that exacerbate pulmonary problems. Nutritional interventions can improve pulmonary functions. We aimed to evaluate the effects of nutritional intervention in CF patients with malnutrition, and to determine if there is a correlation between nutritional status and pulmonary functions.MethodsThe study included 143 CF patients (67 females) with a mean 2 year follow‐up time. Patients’ sociodemographic data, presenting symptoms and history were recorded. Height‐for‐age, weight‐for‐age, weight‐for‐length/height (WFL/H), and body mass index (BMI) were calculated in all patients. Patients were grouped as well nourished, mild malnutrition, moderate malnutrition, and severe malnutrition. These four groups were compared in terms of pulmonary function test results, lung infections, and the hospitalization rate.ResultsAmong the patients with a WFL/H or BMI z‐scores that decreased, the frequency of lung infection was 74.1% and the hospitalization rate was 40.7%, versus 34% and 12.3%, respectively among the patients with a WFL/H or BMI z‐scores that increased. The difference was significant (P = 0.02 and P = 0.01, respectively). The difference in bacterial lung infections differed significantly between the four nutritional status groups (P = 0.002). Patients in the well‐nourished group had significantly higher pulmonary function test scores than the other groups. The forced expiratory volume in the first second differed significantly between the patients with and without an increase in the WFL/H or BMI z‐scores (P = 0.001).ConclusionsThe appropriate nutritional intervention to pediatric CF patients with malnutrition, decrease the frequency of lung infections, and improve respiratory function.
Breast complaints in children and the effect of family history
Authors: Koksal Hande , Ates Dervis , Kara Buket 
Published: August 2020

AbstractBackgroundTo evaluate the correlation of physical examination, and radiological and pathological findings of children and adolescents with breast‐related complaints.MethodsChildren and adolescents with breast complaints between January 2016 and December 2019 were analyzed retrospectively.ResultsA total of 118 children and adolescent patients were included. Their ages ranged from 12 to 18 years (median, 16 years). Twenty‐one patients had a family history of breast cancer (17.8%). The most common complaints were pain, mass, and nipple discharge. Physical examination revealed mass (41.5%), tenderness (11%), and fullness (8.5%). Thirty‐nine patients were classified ultrasonographically with Breast Imaging Reporting and Data System (BIRADS) 3 (39.4%) and four patients were BIRADS 4 (4%). Excision was applied to all patients with BIRADS 4, and 13 of 39 patients with BIRADS 3. Pathological diagnoses of the patients with BIRADS 3 were fibroadenoma (n: 12, 92.3%) and benign phyllodes tumor (n: 1, 7.7%). In patients with BIRADS 4, three patients had fiboradenomas and one patient had a benign phyllodes tumor. No recurrence was observed in any patients who had an excision. Only six of the patients with positive family history had BIRADS 3 lesions, and the others were BIRADS 1. Excision was recommended in two patients and the pathological diagnoses were fibroadenoma.ConclusionIn this age group, the most common complaints were pain and mass, while physical examination was normal in nearly half of the patients. All of the pathological diagnoses were benign. While evaluating the patients in this age range, the experience of the clinician and radiologist is important and we think that it is necessary to increase the awareness of the patient and family about physiological breast development and self‐breast examination.
Virus‐like particles expressing Plasmodium berghei MSP‐8 induce protection against P. berghei infection
Authors: Lee Su‐Hwa , Chu Ki‐Back , Kang Hae‐Ji , Basak Swarnendu , Kim Min‐Ju , Park Hyunwoo , Jin Hui , Moon Eun‐Kyung , Quan Fu‐Shi 
Published: August 2020

AbstractAimsMerozoite surface protein 8 (MSP‐8) of Plasmodium parasites plays an important role in erythrocyte invasion and is a potential malaria vaccine candidate.Methods and ResultsIn this study, virus‐like particles (VLPs) expressing MSP‐8 of Plasmodium berghei on the surface of influenza virus matrix protein 1 (M1) core protein were generated for vaccine efficacy assessment. Mice were intramuscularly (IM) immunized with MSP‐8 VLPs twice and challenge‐infected with P. berghei. We found that VLP vaccination elicited higher levels of P. berghei‐specific IgG antibody response in the sera, along with blood CD4+ and CD8+ T‐cell response enhancement compared to the naïve control mice. CD4+ and CD8+ effector memory T‐cell and memory B‐cell responses in the spleen were found to be higher in VLP‐immunized mice compared to control mice. VLP vaccination significantly reduced inflammatory cytokine (IFN‐γ) response in the spleen and parasitemia levels in blood compared to naïve control mice.ConclusionsThese results indicate that MSP‐8 containing virus‐like particles could be a vaccine candidate for blood‐stage vaccine design.
RNA‐Seq analysis of the guppy immune response against Gyrodactylus bullatarudis infection
Authors: Konczal Mateusz , Ellison Amy R. , Phillips Karl P. , Radwan Jacek , Mohammed Ryan S. , Cable Joanne , Chadzinska Magdalena 
Published: August 2020

AbstractGyrodactylids are ubiquitous ectoparasites of teleost fish, but our understanding of the host immune response against them is fragmentary. Here, we used RNA‐Seq to investigate genes involved in the primary response to infection with Gyrodactylus bullatarudis on the skin of guppies, Poecilia reticulata, an important evolutionary model, but also one of the most common fish in the global ornamental trade. Analysis of differentially expressed genes identified several immune‐related categories, including IL‐17 signalling pathway and Th17 cell differentiation, cytokine‐cytokine receptor interaction, chemokine signalling pathway, NOD‐like receptor signalling pathway, natural killer cell‐mediated cytotoxicity and pathways involved in antigen recognition, processing and presentation. Components of both the innate and the adaptive immune responses play a role in response to gyrodactylid infection. Genes involved in IL‐17/Th17 response were particularly enriched among differentially expressed genes, suggesting a significant role for this pathway in fish responses to ectoparasites. Our results revealed a sizable list of genes potentially involved in the teleost‐gyrodactylid immune response.
A difference equation approach to Plancherel‐Rotach asymptotics for ‐orthogonal polynomials
Authors: Ismail Mourad , Law Chun‐Kong 
Published: August 2020

AbstractIn this paper, we employ a difference equation approach to study the Plancherel‐Rotach asymptotics of ‐orthogonal polynomials about their largest zeros. Our method for ‐difference equations is an analogue to the turning point problem for Hermite differential equations. It works well in the toy problems of Stieltjes‐Wigert polynomials and ‐Hermite polynomials.
Cold‐inducible RNA‐binding protein (CIRP) in inflammatory diseases: Molecular insights of its associated signalling pathways
Authors: Zhong Peng , Peng Jianye , Yuan Mingjie , Kong Bin , Huang He 
Published: August 2020

AbstractCold‐inducible RNA‐binding protein (CIRP) was previously identified as an intracellular stress‐response protein, which can respond to a variety of stress conditions by changing its expression and regulating mRNA stability through its binding site on the 3′‐UTR of its targeted mRNAs. Recently, extracellular CIRP (eCIRP) was discovered to be present in various inflammatory conditions and could act as a pro‐inflammatory factor. Genetic studies have demonstrated a key role for eCIRP in inflammatory conditions that led to the importance of targeting eCIRP in these diseases. Currently, the underlying mechanism of eCIRP‐induced inflammation is under intensive investigation and several signalling pathways are being explored. Here, we epitomized various signalling pathways that mediate the pro‐inflammatory effects of CIRP and also recapitulated all the CIRP‐derived peptides that can block the interaction between CIRP and its receptors in inflammatory setting.
Immunohistochemical characterization of immune cell infiltration in paediatric and adult Langerhans cell histiocytosis
Authors: Paredes Silvia Elena Yacarini , Almeida Luciana Yamamoto , Trevisan Glauce Lunardelli , Polanco Xiomara Beatriz Jimenez , Silveira Heitor Albergoni , Vilela Silva Evânio , Segato Raquel Assed Bezerra , da Silva Léa Assed Bezerra , Chahud Fernando , León Jorge Esquiche 
Published: August 2020

AbstractLangerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia commonly affecting children with frequent somatic mutations in MAPK pathway genes including BRAFV600E and MAP2K1. Some studies suggest that LCH cells can recruit and modulate inflammatory cells, which could provide reciprocal survival signals. To characterize the immune profile of infiltrating inflammatory cells, and to clarify their participation in LCH pathogenesis, a detailed immunohistochemical analysis was performed. Fifteen (10 children, 5 adults) LCH cases were assessed through macrophage (CD68 and CD163), mature dendritic cell (mDC; CD83 and CD208), regulatory T cell (Treg; CD4, CD25 and FOXP3) and cytotoxic lymphocyte (CL; CD56, CD57, perforin and granzyme B) immunomarkers. Moreover, lymphocytic and LCH markers were also analysed. All cases were S100, CD1a, CD207 and CD4‐positive. Bcl‐2 and cyclin D1 expression was observed in 13 of 15 cases. In the immune microenvironment, M2‐polarized macrophages and Tregs were the predominant cell populations, followed by significantly (P < .005) smaller levels of mDCs and CLs. Additionally, the number of CD3 + cells was significantly higher than that of CD20 + cells. In the CD3 + cell population, there were a significantly higher number of CD4 + cells than CD8 + cells. While there were no differences when comparing the paediatric and adult populations, FOXP3 + cells were significantly higher in patients with multisystem involvement and treated with chemotherapy, than single‐site cases and those without chemotherapy. Our results suggest that M2‐polarized macrophages and Treg infiltration can promote LCH development and survival, probably through pro‐tumoral, immunosuppressive and/or cytokine‐mediated mechanisms. This work highlights the need for further exploration of immune‐targeted therapy for LCH.