bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome analysis of two novel Pseudomonas strains exhibiting differential hypersensitivity reactions on tobacco seedlings reveals differences in nonflagellar T3SS organization and predicted effector proteins
Authors: Tchagang Caetanie F. , Xu Renlin , Doumbou Cyr Lézin , Tambong James T. 
Published: February 2018

AbstractMultilocus sequence analysis (MLSA) of two new biological control strains (S1E40 and S3E12) of Pseudomonas was performed to assess their taxonomic position relative to close lineages, and comparative genomics employed to investigate whether these strains differ in key genetic features involved in hypersensitivity responses (HRs). Strain S3E12, at high concentration, incites HRs on tobacco and corn plantlets while S1E40 does not. Phylogenies based on individual genes and 16S rRNA‐gyrB‐rpoB‐rpoD concatenated sequence data show strains S1E40 and S3E12 clustering in distinct groups. Strain S3E12 consistently clustered with Pseudomonas marginalis, a bacterium causing soft rots on plant tissues. MLSA data suggest that strains S1E40 and S3E12 are novel genotypes. This is consistent with the data of genome‐based DNA‐DNA homology values that are below the proposed cutoff species boundary. Comparative genomics analysis of the two strains revealed major differences in the type III secretion systems (T3SS) as well as the predicted T3SS secreted effector proteins (T3Es). One nonflagellar (NF‐T3SS) and two flagellar T3SSs (F‐T3SS) clusters were identified in both strains. While F‐T3SS clusters in both strains were relatively conserved, the NF‐T3SS clusters differed in the number of core components present. The predicted T3Es also differed in the type and number of CDSs with both strains having unique predicted protease‐related effectors. In addition, the T1SS organization of the S3E12 genome has protein‐coding sequences (CDSs) encoding for key factors such as T1SS secreted agglutinin repeats‐toxins (a group of cytolysins and cytotoxins), a membrane fusion protein (LapC), a T1SS ATPase of LssB family (LapB), and T1SS‐associated transglutaminase‐like cysteine proteinase (LapP). In contrast, strain S1E40 has all CDSs for the seven‐gene operon (pelA‐pelG) required for Pel biosynthesis but not S3E12, suggesting that biofilm formation in these strains is modulated differently. The data presented here provide an insight of the genome organization of these two phytobacterial strains.
Global strong solution to the three dimensional nonhomogeneous incompressible magnetohydrodynamic equations with density‐dependent viscosity and resistivity
Authors: Li Huanyuan 
Published: February 2018

In this paper, we consider an initial boundary value problem for the 3‐dimensional nonhomogeneous incompressible magnetohydrodynamic equations with density‐dependent viscosity and resistivity coefficients over a bounded smooth domain. Global in time unique strong solution is proved to exist when the L2 norms of initial vorticity and current density are both suitably small with arbitrary large initial density, and the vacuum of initial density is also allowed.Finally, we revisit the Navier‐Stokes model without electromagnetic effect. We find that this initial boundary problem also admits a unique global strong solution under other conditions. In particular, we prove small kinetic‐energy strong solution exists globally in time, which extends the recent result of Huang and Wang.
Effects of Different Lipid Sources on Growth and Fatty Acid Composition of Juvenile Triangular Bream Megalobrama terminalis
Authors: Tian Hanlin , Wang Jiteng , Han Tao , Yang Min , Xu Hanying , Sheng Jianhai , Zheng Puqiang 
Published: February 2018

Abstract
Five diets containing lipids from different sources, namely fish oil (FO), soybean oil (SO), linseed oil (LO), rapeseed (canola) oil (RO), and palm oil (PO), were fed to juvenile Triangular Bream Megalobrama terminalis (initially weight, 1.20 ± 0.02 g) for 70 d. At the end of the feeding trial, weight gain (WG), specific growth rate (SGR), feed conversion ratio (FCR), and daily feed intake (DFI) were not significantly different among all treatments. The retention rates of C22:6(n-3) (docosahexaenoic acid [DHA]) in fish fed LO-based (143.8%) diets were significantly higher than in those fed FO-based (61.0%) diet. Moreover, fish fed LO-based diet showed a significantly higher C20:5(n-3) (eicosapentaenoic acid [EPA]) content (1.6%) in the liver than fish fed SO-, RO-, and PO-based (1.1, 0.9, and 0.9%, respectively) diets. The retention rates of C20:4(n-6) (arachidonic acid [ARA]) in fish fed RO-based (341.3%) diets were significantly higher than in those fed FO-, LO-, and PO-based (87.3, 176.8, and 216.3%, respectively) diets, while fish fed SO- and RO-based diets had significantly higher ARA concentrations in the liver than did fish fed FO-based diet. The fatty acid compositions of fish tissues were significantly affected by different lipid sources. Fish fed vegetable oil (VO) diets had lower n-3 long-chain polyunsaturated fatty acid (LC-PUFAs) concentrations in dorsal muscles than did fish in the FO group (18.4%), and significant differences were detected in fish fed SO (10.1%) and RO (10.9%) diets. These results showed that Triangular Bream have an ability to synthesize DHA, EPA, and ARA from alpha-linolenic acid (ALA) and linoleic acid (LA). However, fish fed VO-based diets could reduce the nutritional value of the fish flesh.
Influence of length effect on embankment slope reliability in 3D
Authors: Hicks Michael A. , Li Yajun 
Published: February 2018

SummaryEmbankment slopes composed of spatially variable soils have a variety of different failure modes that are affected by the correlation distances of the material properties and the geometry and total length of the slope. This paper examines the reliability of soil slopes for embankments of different length and uses parallel computing to analyse very long embankments (up to 100 times the embankment height) for a clay soil characterised by a spatially varying undrained shear strength. Based on a series of analyses using the 3D random finite element method (RFEM), it is first shown that the reliability of slopes of various length can be efficiently computed by combining simple probability theory with a detailed 3D RFEM analysis of a representative shorter slope of length 10 times the slope height. RFEM predictions of reliability indices for longer slopes are then compared with results obtained using Vanmarcke's (1977a) simplified 3D method and Calle's (1985) extended 2D approach. It is shown that these methods can give significantly different results, depending on the horizontal scale of fluctuation relative to the slope length, with RFEM predicting a lower slope reliability than the Vanmarcke and Calle solutions in all cases. The differences in the solutions are evaluated and attributed to differences in the assumed and computed failure surface geometries.
Revisiting the existence of an effective stress for wet granular soils with micromechanics
Authors: Duriez Jérôme , Wan Richard , Pouragha Mehdi , Darve Félix 
Published: February 2018

SummaryA possible effective stress variable for wet granular materials is numerically investigated based on an adapted discrete element method (DEM) model for an ideal three‐phase system. The DEM simulations consider granular materials made of nearly monodisperse spherical particles, in the pendular regime with the pore fluid mixture consisting of distinct water menisci bridging particle pairs. The contact force‐related stress contribution to the total stresses is isolated and tested as the effective stress candidate for dense or loose systems. It is first recalled that this contact stress tensor is indeed an adequate effective stress that describes stress limit states of wet samples with the same Mohr‐Coulomb criterion associated with their dry counterparts. As for constitutive relationships, it is demonstrated that the contact stress tensor used in conjunction with dry constitutive relations does describe the strains of wet samples during an initial strain regime but not beyond. Outside this so‐called quasi‐static strain regime, whose extent is much greater for dense than loose materials, dramatic changes in the contact network prevent macroscale contact stress‐strain relationships to apply in the same manner to dry and unsaturated conditions. The presented numerical results also reveal unexpected constitutive bifurcations for the loose material, related to stick‐slip macrobehavior.
Bifurcation analysis of nonlinear time‐periodic time‐delay systems via semidiscretization
Authors: Molnar T. G. , Dombovari Z. , Insperger T. , Stepan G. 
Published: February 2018

SummaryBifurcations of the periodic stationary solutions of nonlinear time‐periodic time‐delay dynamical systems are analyzed. The solution operator of the governing nonlinear delay‐differential equation is approximated by a sequence of nonlinear maps via semidiscretization. The subsequent nonlinear maps are combined to a single resultant nonlinear map that describes the evolution over the time period. Fold, flip, and Neimark‐Sacker bifurcations related to the fixed point of this map are analyzed via center manifold reduction and normal form theorems. The analysis unfolds the approximate stability properties and bifurcations of the stationary solution of the delay‐differential equation and, at the same time, allows the approximate computation of the arising period‐1, period‐2, and quasi‐periodic solution branches. The method is demonstrated for the delayed Mathieu‐Duffing equation, and the results are verified by numerical continuation.
Hydroxylysine deficiency, conspicuous skeletal lesions and a strange burial practice in a historical German island population
Authors: Burkhardt A. , Grupe G. 
Published: February 2018

AbstractEighty‐two complete and partial human skeletons were excavated from a burial site on the island of Borkum in the North Sea. The site covers a period of 400 years from the middle of the 14th century AD until 1720 AD. The position of the skeletons in situ suggests rapid disposal of the bodies. About 75% of the skeletons were male and of a quite robust constitution, and about 60% of all individuals died rather young between 20 and 40 years of age. All male skeletons exhibited particular pathological alterations as a result of the typical daily activities of seafaring men, including severe degenerative joint disease and pronounced osteochondropathies. In juvenile skeletons, these pathologies were accompanied by inflammatory processes without exception. Palaeodietary reconstruction by stable isotope analysis resulted in a protein rich diet, confirming fishing as an important part of the subsistence economy. The juveniles derived substantially more protein from plant food than the adults. Bone collagen amino acid profiles were short of hydroxylysine, suggesting that the conspicuous pathological lesions could also have been caused by a systemic connective tissue disease. Possible etiology of the disease is discussed and related to both the uneven sex ratio of the inhumations and the burial context.
Richter transformation driven by Epstein–Barr virus reactivation during therapy‐related immunosuppression in chronic lymphocytic leukaemia
Authors: García‐Barchino Maria J , Sarasquete Maria E , Panizo Carlos , Morscio Julie , Martinez Antonio , Alcoceba Miguel , Fresquet Vicente , Gonzalez‐Farre Blanca , Paiva Bruno , Young Ken H , Robles Eloy F , Roa Sergio , Celay Jon , Larrayoz Marta , Rossi Davide , Gaidano Gianluca , Montes‐Moreno Santiago , Piris Miguel A , Balanzategui Ana , Jimenez Cristina , Rodriguez Idoia , Calasanz Maria J , Larrayoz Maria J , Segura Victor , Garcia‐Muñoz Ricardo , Rabasa Maria P , Yi Shuhua , Li Jianyong , Zhang Mingzhi , Xu‐Monette Zijun Y , Puig‐Moron Noemi , Orfao Alberto , Böttcher Sebastian , Hernandez‐Rivas Jesus M , Miguel Jesus San , Prosper Felipe , Tousseyn Thomas , Sagaert Xavier , Gonzalez Marcos , Martinez‐Climent Jose A 
Published: February 2018

AbstractThe increased risk of Richter transformation (RT) in patients with chronic lymphocytic leukaemia (CLL) due to Epstein–Barr virus (EBV) reactivation during immunosuppressive therapy with fludarabine other targeted agents remains controversial. Among 31 RT cases classified as diffuse large B‐cell lymphoma (DLBCL), seven (23%) showed EBV expression. In contrast to EBV– tumours, EBV+ DLBCLs derived predominantly from IGVH‐hypermutated CLL, and they also showed CLL‐unrelated IGVH sequences more frequently. Intriguingly, despite having different cellular origins, clonally related and unrelated EBV+ DLBCLs shared a previous history of immunosuppressive chemo‐immunotherapy, a non‐germinal centre DLBCL phenotype, EBV latency programme type II or III, and very short survival. These data suggested that EBV reactivation during therapy‐related immunosuppression can transform either CLL cells or non‐tumoural B lymphocytes into EBV+ DLBCL. To investigate this hypothesis, xenogeneic transplantation of blood cells from 31 patients with CLL and monoclonal B‐cell lymphocytosis (MBL) was performed in Rag2–/– IL2γc–/– mice. Remarkably, the recipients' impaired immunosurveillance favoured the spontaneous outgrowth of EBV+ B‐cell clones from 95% of CLL and 64% of MBL patients samples, but not from healthy donors. Eventually, these cells generated monoclonal tumours (mostly CLL‐unrelated but also CLL‐related), recapitulating the principal features of EBV+ DLBCL in patients. Accordingly, clonally related and unrelated EBV+ DLBCL xenografts showed indistinguishable cellular, virological and molecular features, and synergistically responded to combined inhibition of EBV replication with ganciclovir and B‐cell receptor signalling with ibrutinib in vivo. Our study underscores the risk of RT driven by EBV in CLL patients receiving immunosuppressive therapies, and provides the scientific rationale for testing ganciclovir and ibrutinib in EBV+ DLBCL. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Brincidofovir as Salvage Therapy for Adenovirus Disease in Intestinal Transplant Recipients
Authors: Sulejmani Nimisha , Nagai Shunji , Safwan Mohamed , Rizzari Michael D. , Raoufi Mohammad , Abouljoud Marwan S. , Ramesh Mayur 
Published: February 2018

BackgroundAdenoviruses are double‐stranded DNA viruses that typically cause mild self‐limiting respiratory, ocular, and gastrointestinal infections. In immunocompromised patients, especially transplant recipients, the infection can be severe, with dissemination and multiorgan failure. In intestinal transplant recipients, the incidence is as high as 57%. To our knowledge, no standardized guidelines or U.S. Food and Drug Administration–approved medications exist for the treatment of adenovirus disease.AimsWe describe two isolated intestinal transplant recipients who developed adenovirus disease (viremia with viral enteritis) that was managed with a new experimental drug, brincidofovir (an oral lipid conjugate prodrug of cidofovir), as salvage therapy.ResultsThe first patient was a 44‐year‐old woman who developed adenoviral enteritis 1 month after transplantation, which resolved with ribavirin therapy. Two weeks later, the infection recurred, and brincidofovir was initiated. While receiving this therapy for 3 months, she developed severe acute rejection, which was managed with rabbit antithymocyte globulin followed by infliximab. Eventually, complete resolution of the rejection and adenoviral enteritis was achieved. At 12 months posttransplantation, the patient was healthy and tolerating enteral feeding. The second patient was a 28‐year‐old man who had undergone isolated intestinal transplantation 6 years before he presented with generalized weakness and an increased ostomy output; he was diagnosed with adenoviral enteritis. Maintenance immunosuppression was reduced, and brincidofovir was started. The infection resolved with a month of therapy. Six months after the infection, he was healthy and tolerating enteral feeding.ConclusionThis is the first publication, to our knowledge, to describe two cases in which brincidofovir was used to successfully treat adenovirus infection in intestinal transplant recipients. Thus, these cases demonstrate that brincidofovir appears to be a safe and effective option in the management of adenoviral enteritis in these patients.
A Multi‐Omics Analysis of Glycine max Leaves Reveals Alteration in Flavonoid and Isoflavonoid Metabolism Upon Ethylene and Abscisic Acid Treatment
Authors: Gupta Ravi , Min Cheol Woo , Kramer Katharina , Agrawal Ganesh Kumar , Rakwal Randeep , Park Ki‐Hun , Wang Yiming , Finkemeier Iris , Kim Sun Tae 
Published: February 2018

AbstractPhytohormones are central to plant growth and development. Despite the advancement in our knowledge of hormone signaling, downstream targets, and their interactions upon hormones action remain largely fragmented, especially at the protein and metabolite levels. With an aim to get new insight into the effects of two hormones, ethylene (ET) and abscisic acid (ABA), this study utilizes an integrated proteomics and metabolomics approach to investigate their individual and combined (ABA+ET) signaling in soybean leaves. Targeting low‐abundance proteins, our previously established protamine sulfate precipitation method was applied, followed by label‐free quantification of identified proteins. A total of 4129 unique protein groups including 1083 differentially modulated in one (individual) or other (combined) treatments were discerned. Functional annotation of the identified proteins showed an increased abundance of proteins related to the flavonoid and isoflavonoid biosynthesis and MAPK signaling pathway in response to ET treatment. HPLC analysis showed an accumulation of isoflavones (genistin, daidzein, and genistein) upon ET treatment, in agreement with the proteomics results. A metabolome analysis assigned 79 metabolites and further confirmed the accumulation of flavonoids and isoflavonoids in response to ET. A potential cross‐talk between ET and MAPK signaling, leading to the accumulation of flavonoids and isoflavonoids in soybean leaves is suggested.
Protein Network Analysis and Functional Studies of Calcium Oxalate Crystal‐Induced Cytotoxicity in Renal Tubular Epithelial Cells
Authors: Peerapen Paleerath , Chaiyarit Sakdithep , Thongboonkerd Visith 
Published: February 2018

AbstractOur previous expression study has reported a set of proteins with altered levels in renal tubular cells after exposure to calcium oxalate monohydrate (COM) crystals, which are the main composition of kidney stones. However, their functional significance remained largely unknown. In this study, protein network analysis revealed that the significantly altered proteins induced by COM crystals were involved mainly in three main functional networks, including i) cell proliferation and wound healing; ii) oxidative stress and mitochondrial function; and iii) cellular junction complex and integrity. Cell proliferation and wound healing assays showed that the COM‐treated cells had defective proliferation and tissue healing capability, respectively. Oxyblot analysis demonstrated accumulation of the oxidized proteins, whereas intracellular ATP level was significantly increased in the COM‐treated cells. Additionally, level of zonula occludens‐1 (ZO‐1), a tight junction protein, was significantly decreased, consistent with the significant declines in transepithelial resistance (TER) and level of RhoA signaling molecule in the COM‐treated cells. These findings indicate significant perturbations in mitochondrial and oxidative stress axis that cause defective cell proliferation, tissue healing capability, junctional protein complex, and cellular integrity of renal tubular epithelial cells exposed to COM crystals that may play important roles in kidney stone pathogenesis.
Respiratory syncytial virus is an “opportunistic” killer
Authors: Caballero Mauricio T. , Polack Fernando P. 
Published: February 2018

AbstractRespiratory syncytial virus (RSV), responsible for more than three million yearly hospitalizations and up to 118 000 deaths in children under 5 years, is the leading pulmonary cause of death for this age group that lacks a licensed vaccine. Ninety‐nine percent of deaths due to the virus occur in developing countries. In‐hospital RSV fatalities affect previously healthy term infants in association with bacterial sepsis, clinically significant pneumothoraxes and, to a lesser extent, comorbid conditions. Community deaths affect low‐income children from socially vulnerable families and appear to be as frequent as inpatient fatalities. In industrialized countries, RSV deaths occur almost exclusively in children with premorbid conditions.In a sense, RSV is an “opportunistic” killer. It needs a synergistic premorbid, medical practice‐related, infectious, or social co‐factor to cause a fatal outcome. But while the complex problems associated with these co‐factors await solutions, candidate vaccines, long‐lived monoclonal antibodies and antivirals against RSV are under clinical evaluation. It seems reasonable to predict that the landscape of RSV infections will look different in the next decade.
Medication adherence in pediatric asthma: A systematic review of the literature
Authors: Gray Wendy N. , Netz Mallory , McConville Andrew , Fedele David , Wagoner Scott T. , Schaefer Megan R. 
Published: February 2018

AbstractObjectiveTo provide a systematic review of correlates of adherence to inhaled corticosteroids (ICS) in pediatric asthma across the individual, family, community, and healthcare system domains.MethodsArticles assessing medication adherence in pediatric asthma published from 1997 to 2016 were identified using PsychINFO, Medline, and CINAHL. Search terms included asthma, compliance, self‐management, adherence, child, and youth. Search results were limited to articles: 1) published in the US; 2) using a pediatric population (0‐25 years old); and 3) presenting original data related to ICS adherence. Correlates of adherence were categorized according to the domains of the Pediatric Self‐Management Model. Each article was evaluated for study quality.ResultsSeventy‐nine articles were included in the review. Family‐level correlates were most commonly reported (N = 51) and included socioeconomic status, race/ethnicity, health behaviors, and asthma knowledge. Individual‐level correlates were second‐most common (N = 37), with age being the most frequently identified negative correlate of adherence. Health care system correlates (N = 24) included enhanced asthma care and patient‐provider communication. Few studies (N = 10) examined community correlates of adherence. Overall study quality was moderate, with few quantitative articles (26.38%) and qualitative articles (21.4%) referencing a theoretical basis for their studies.ConclusionsAll Pediatric Self‐Management Model domains were correlated with youth adherence, which suggests medication adherence is influenced across multiple systems; however, most studies assessed adherence correlates within a single domain. Future research is needed that cuts across multiple domains to advance understanding of determinants of adherence.