bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a genome-informed loop-mediated isothermal amplification assay for rapid and specific detection of Xanthomonas euvesicatoria
Authors: Larrea-Sarmiento Adriana , Dhakal Upasana , Boluk Gamze , Fatdal Lilly , Alvarez Anne , Strayer-Scherer Amanda , Paret Mathews , Jones Jeff , Jenkins Daniel , Arif Mohammad 
Published: September 2018

AbstractBacterial spot (BS), caused by Xanthomonas euvesicatoria, X. vesicatoria, X. gardneri and X. perforans, is an economically important bacterial disease of tomato and pepper. Symptoms produced by all four species are nearly indistinguishable. At present, no point-of-care diagnostics exist for BS. In this research, we examined genomes of X. euvesicatoria, X. vesicatoria, X. gardneri, X. perforans and other species of Xanthomonas; the unique gene recG was chosen to design primers to develop a loop-mediated isothermal amplification (LAMP) assay to rapidly and accurately identify and differentiate X. euvesicatoria from other BS causing Xanthomonas sp. using a field-deployable portable BioRangerTM instrument. Specificity of the developed assay was tested against 39 strains of X. euvesicatoria and 41 strains of other species in inclusivity and exclusivity panels, respectively. The assay detection limit was 100 fg (~18 genome copies) of genomic DNA and 1,000 fg in samples spiked with tomato DNA. The assay unambiguously detected X. euvesicatoria in infected tomato plant samples. Concordant results were obtained when multiple operators performed the test independently. No false positives and false negatives were detected. The developed LAMP assay has numerous applications in diagnostics, biosecurity and disease management.
GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle
Authors: Higgins Marc G. , Fitzsimons Claire , McClure Matthew C. , McKenna Clare , Conroy Stephen , Kenny David A. , McGee Mark , Waters Sinéad M. , Morris Derek W. 
Published: September 2018

AbstractResidual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10−5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.
Dendritic cell maturation in the corneal epithelium with onset of type 2 diabetes is associated with tumor necrosis factor receptor superfamily member 9
Authors: Lagali Neil S. , Badian Reza A. , Liu Xu , Feldreich Tobias R. , Ärnlöv Johan , Utheim Tor Paaske , Dahlin Lars B. , Rolandsson Olov 
Published: September 2018

AbstractType 2 diabetes mellitus is characterized by a low-grade inflammation; however, mechanisms leading to this inflammation in specific tissues are not well understood. The eye can be affected by diabetes; thus, we hypothesized that inflammatory changes in the eye may parallel the inflammation that develops with diabetes. Here, we developed a non-invasive means to monitor the status of inflammatory dendritic cell (DC) subsets in the corneal epithelium as a potential biomarker for the onset of inflammation in type 2 diabetes. In an age-matched cohort of 81 individuals with normal and impaired glucose tolerance and type 2 diabetes, DCs were quantified from wide-area maps of the corneal epithelial sub-basal plexus, obtained using clinical in vivo confocal microscopy (IVCM). With the onset of diabetes, the proportion of mature, antigen-presenting DCs increased and became organized in clusters. Out of 92 plasma proteins analysed in the cohort, tumor necrosis factor receptor super family member 9 (TNFRSF9) was associated with the observed maturation of DCs from an immature to mature antigen-presenting phenotype. A low-grade ocular surface inflammation observed in this study, where resident immature dendritic cells are transformed into mature antigen-presenting cells in the corneal epithelium, is a process putatively associated with TNFRSF9 signalling and may occur early in the development of type 2 diabetes. IVCM enables this process to be monitored non-invasively in the eye.
High resolution 7T and 9.4T-MRI of human cerebral arterial casts enables accurate estimations of the cerebrovascular morphometry
Authors: Helthuis Jasper H. G. , van der Zwan Albert , van Doormaal Tristan P. C. , Bleys Ronald L. A. W. , Harteveld Anita A. , van der Toorn Annette , Brozici Mariana , Hendrikse Jeroen , Zwanenburg Jaco J. M. 
Published: September 2018

AbstractQuantitative data on the morphology of the cerebral arterial tree could aid in modelling and understanding cerebrovascular diseases, but is scarce in the range between 200 micrometres and 1 mm diameter arteries. Traditional manual measurements are difficult and time consuming. 7T-MRI and 9.4T-MRI of human cerebral arterial plastic casts could proof feasible for acquiring detailed morphological data of the cerebral arterial tree in a time efficient method. One cast of the complete human cerebral arterial circulation embedded in gadolinium-containing gelatine gel was scanned at 7T-MRI (0.1 mm isotropic resolution). A small section of another cast was scanned at 9.4T-MRI (30 µm isotropic resolution). Subsequent 3D-reconstruction was performed using a semi-automatic approach. Validation of 7T-MRI was performed by comparing the radius calculated using MRI to manual measurements on the same cast. As manual measurement of the small section was not feasible, 9.4T-MRI was validated by scanning the small section both at 7T-MRI and 9.4T MRI and comparing the diameters of arterial segments. Linear regression slopes were 0.97 (R-squared 0.94) and 1.0 (R-squared 0.90) for 7T-MRI and 9.4T-MRI. This data shows that 7T-MRI and 9.4T-MRI and subsequent 3D reconstruction of plastic casts is feasible, and allows for characterization of human cerebral arterial tree morphology.
Novel role for receptor dimerization in post-translational processing and turnover of the GRα
Authors: Wilkinson Legh , Verhoog Nicolette , Louw Ann 
Published: September 2018

AbstractGlucocorticoids (GCs), acting via the glucocorticoid receptor (GRα), remain the mainstay therapeutic choice for the treatment of inflammation. However, chronic GC use, aside from generating undesirable side-effects, results in GRα down-regulation, often coupled to a decrease in GC-responsiveness, which may culminate in acquired GC resistance. The current study presents evidence for a novel role of the dimerization state of the GRα in mediating GC-mediated GRα turnover. Through comparing the effects of dimerization promoting GCs on down-regulation of a transfected human wild type GRα (hGRwt) or a dimerization deficient GRα mutant (hGRdim), we established that a loss of receptor dimerization restricts GRα turnover, which was supported by the use of the dimerization abrogating Compound A (CpdA), in cells containing endogenous GRα. Moreover, we showed that the dimerization state of the GRα influenced the post-translational processing of the receptor, specifically hyper-phosphorylation at Ser404, which influenced the interaction of GRα with the E3 ligase, FBXW7α, thus hampering receptor turnover via the proteasome. Lastly, the restorative effects of CpdA on the GRα pool, in the presence of Dex, were demonstrated in a combinatorial treatment protocol. These results expand our understanding of factors that contribute to GC-resistance and may be exploited clinically.
Reversible Human Immunodeficiency Virus Type-1 Latency in Primary Human Monocyte-Derived Macrophages Induced by Sustained M1 Polarization
Authors: Graziano Francesca , Aimola Giulia , Forlani Greta , Turrini Filippo , Accolla Roberto S. , Vicenzi Elisa , Poli Guido 
Published: September 2018

AbstractWe have reported that short-term stimulation of primary human monocyte-derived macrophages (MDM) with interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α), i.e. M1 polarization, leads to a significant containment of virus replication. Here we show that M1-MDM restimulation with these cytokines 7 days after infection (M12MDM) promoted an increased restriction of HIV-1 replication characterized by very low levels of virus production near to undetectable levels. In comparison to control and M1-MDM that were not restimulated, M12MDM showed a stronger reduction of both total and integrated HIV DNA as well as of viral mRNA expression. M12MDM were characterized by an upregulated expression of restriction factors acting at the level of reverse transcription (RT), including apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A (APOBEC3A) and APOBEC3G, but not SAM domain and HD domain-containing protein 1 (SAMHD1). M12MDM also showed an increased expression of Class II Transactivator (CIITA) and Tripartite Motif22 (TRIM22), two negative regulators of proviral transcription, whereas expression and phosphorylation of transcriptional inducers of HIV-1, such as nuclear factor kB (NF-kB) and signal transducer and activator of transcription 1 (STAT1), were not impaired in these cells. The almost quiescent state of the infection in M12MDM was promptly reversed by coculture with mitogen-stimulated leukocytes or cell incubation with their filtered culture supernatant. M12MDM harbored replication-competent HIV-1 as virus spreading following cell stimulation was fully prevented by the RT inhibitor lamivudine/3TC. Selective reactivation of proviral expression in M12MDM, but not in control or in M1-MDM that were not restimulated, was confirmed in cells infected with single round Vesicular Stomatitis Virus-G-pseudotyped HIV-1. Thus, M12MDM represent anin vitromodel of reversible, almost quiescent HIV-1 infection of primary human macrophages that could be further exploited for “Cure” related investigations.
The modification and characterization of thermal-treated sericite by fluorosilicate
Authors: Liang Yu , Jiang Wei , Ding Hao , Wang Yongkui 
Published: September 2018

AbstractIn this article, the thermal-treated sericite was modified by both fluorosilicate and the combination of fluorosilicate and nitric acid in order to reduce its layer charge and gain cation exchange capabilities for the preparation of sericite/polymer nanocomposites. After several orthogonal experiments and single factor experiments, the optimal experimental conditions were set up and we found that the combination of nitric acid and fluorosilicate is much more effective than fluorosilicate alone. Chemical composition analysis showed Al3+ was dissolved out from sericite and the dissolving amount is 65 mg/g under optimal experimental conditions. Combining the NMR test, it is considered that the Si/Al ratio in the tetrasheet of the modified product increased from 3.48 to 10. The layer charge reduced and the CEC value increased after fluorosilicate modification, which means the modified sericite is a promising matrix for clay-polymer nanocomposites.
Speckle tracking-derived bi-atrial strain before and after eleven weeks of training in elite rowers
Authors: Sareban Mahdi , Winkert Kay , Sperlich Billy , Berger Marc M. , Niebauer Josef , Steinacker Jürgen M. , Treff Gunnar 
Published: September 2018

AbstractThe left (LA) and right (RA) atria undergo adaptive remodeling in response to hemodynamic stress not only induced by endurance exercise but also as part of several cardiovascular diseases thereby confounding differential diagnosis. Echocardiographic assessment of the atria with novel speckle tracking (STE)-derived variables broadens the diagnostic spectrum compared to conventional analyses and has the potential to differentiate physiologic from pathologic changes. The purpose of this study was to assess and categorize baseline values of bi-atrial structure and function in elite rowers according to recommended cutoffs, and to assess the cardiac changes occurring with endurance training. Therefore, fifteen elite rowers underwent 2D-echocardiographic analysis of established variables of cardiac structure and function as well as STE-derived variables of bi-atrial function. Measurements were performed at baseline and after eleven weeks of extensive training. 40% of athletes displayed mildly enlarged LA and 47% mildly enlarged RA at baseline, whereas no athlete fell below the lower reference values of LA and RA reservoir strain. Average power during a 2000 m ergometer rowing test (P2000 m) improved from 426 ± 39 W to 442 ± 34 W (p = 0.010) but there were no changes of echocardiographic variables following training. In elite rowers, longitudinal bi-atrial strain assessment indicates normal resting function of structurally enlarged atria and thereby may assist to differentiate between exercise-induced versus disease-associated structural cardiac changes in which function is commonly impaired.
Identification of a limb enhancer that is removed by pathogenic deletions downstream of the SHOX gene
Authors: Skuplik Isabella , Benito-Sanz Sara , Rosin Jessica M. , Bobick Brent E. , Heath Karen E. , Cobb John 
Published: September 2018

AbstractHaploinsufficiency of the human SHOX gene causes Léri-Weill dyschondrosteosis (LWD), characterized by shortening of the middle segments of the limbs and Madelung deformity of the wrist. As many as 35% of LWD cases are caused by deletions of non-coding sequences downstream of SHOX that presumably remove an enhancer or enhancers necessary for SHOX expression in developing limbs. We searched for these active sequences using a transgenic mouse assay and identified a 563 basepair (bp) enhancer with specific activity in the limb regions where SHOX functions. This enhancer has previously escaped notice because of its poor evolutionary conservation, although it does contain 100 bp that are conserved in non-rodent mammals. A primary cell luciferase assay confirmed the enhancer activity of the conserved core sequence and demonstrated that putative HOX binding sites are required for its activity. This enhancer is removed in most non-coding deletions that cause LWD. However, we did not identify any likely pathogenic variants of the enhancer in a screen of 124 LWD individuals for whom no causative mutation had been found, suggesting that only larger deletions in the region commonly cause LWD. We hypothesize that loss of this enhancer contributes to the pathogenicity of deletions downstream of SHOX.
Enantiomeric Aβ peptides inhibit the fluid shear stress response of PIEZO1
Authors: Maneshi Mohammad M. , Ziegler Lynn , Sachs Frederick , Hua Susan Z. , Gottlieb Philip A. 
Published: September 2018

AbstractTraumatic brain injury (TBI) elevates Abeta (Aβ) peptides in the brain and cerebral spinal fluid. Aβ peptides are amphipathic molecules that can modulate membrane mechanics. Because the mechanosensitive cation channel PIEZO1 is gated by membrane tension and curvature, it prompted us to test the effects of Aβ on PIEZO1. Using precision fluid shear stress as a stimulus, we found that Aβ monomers inhibit PIEZO1 at femtomolar to picomolar concentrations. The Aβ oligomers proved much less potent. The effect of Aβs on Piezo gating did not involve peptide-protein interactions since the D and L enantiomers had similar effects. Incubating a fluorescent derivative of Aβ and a fluorescently tagged PIEZO1, we showed that Aβ can colocalize with PIEZO1, suggesting that they both had an affinity for particular regions of the bilayer. To better understand the PIEZO1 inhibitory effects of Aβ, we examined their effect on wound healing. We observed that over-expression of PIEZO1 in HEK293 cells increased cell migration velocity ~10-fold, and both enantiomeric Aβ peptides and GsMTx4 independently inhibited migration, demonstrating involvement of PIEZO1 in cell motility. As part of the motility study we examined the correlation of PIEZO1 function with tension in the cytoskeleton using a genetically encoded fluorescent stress probe. Aβ peptides increased resting stress in F-actin, and is correlated with Aβ block of PIEZO1-mediated Ca2+ influx. Aβ inhibition of PIEZO1 in the absence of stereospecific peptide-protein interactions shows that Aβ peptides modulate both cell membrane and cytoskeletal mechanics to control PIEZO1-triggered Ca2+ influx.
Effectiveness of monovalent rotavirus vaccine in the Philippines
Authors: Lopez Anna Lena , Daag Jedas Veronica , Esparagoza Joel , Bonifacio Joseph , Fox Kimberley , Nyambat Batmunkh , Parashar Umesh D. , Ducusin Maria Joyce , Tate Jacqueline E. 
Published: September 2018

AbstractRotavirus (RV) is an important cause of diarrheal disease particularly in children aged under 5 years. Monovalent RV vaccine (RVV) was selectively introduced in 2012 in the Philippines and in July 2014 was introduced in the public health program of a province. Two RVV doses are recommended at 6 and 10 weeks of age. We conducted a test negative case-control evaluation to assess the effectiveness of RVV when given in a routine public health program in the Philippines. From September 2014 to August 2017, 967 children aged <5 years were hospitalized with diarrhea and of these, we enrolled 600 who were eligible to have received RVV and provided stool specimens for testing. Among children ≥8 months of age who were age-eligible to have received RVV, at least one dose of RVV had an adjusted vaccine effectiveness (VE) against RV hospitalization of 60% (95% confidence interval, CI: 24%, 79%), and against severe rotavirus diarrhea, VE was 64% (95% CI: 11%, 85%). These findings support the introduction of RVV into routine public health use in the Philippines. However, other factors such as costs, cost-effectiveness and operational issues must be considered prior to adoption of the vaccine into the countries’ public immunization program.
Transcriptomic insights into the blue light-induced female floral sex expression in cucumber (Cucumis sativus L.)
Authors: Zhou Yong , Ahammed Golam Jalal , Wang Qiang , Wu Chaoqun , Wan Chunpeng , Yang Youxin 
Published: September 2018

AbstractIn cucurbitaceous crops, sex differentiation of flower buds is a crucial developmental process that directly affects fruit yield. Here we showed that the induction of female flower was the highest in the blue light-treated monoecious cucumber plants compared with that in other light qualities (white, green and red). High-throughput RNA-Seq analysis of the shoot apexes identified a total of 74 differently-expressed genes (DEGs), in which 52 up-regulated and 22 down-regulated under the blue light compared with that in white light. The DEGs were mainly involved in metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction, starch and sucrose metabolism and phenylpropanoid biosynthesis. While the ethylene and gibberellins synthesis and signaling related genes were down-regulated, the abscisic acid and auxin signal transduction pathways were up-regulated by the blue light treatment. Furthermore, the blue light treatment up-regulated the transcription of genes relating to photosynthesis, starch and sucrose metabolism. Meanwhile, the blue light suppressed the GA3 concentration but promoted the concentrations of auxin and photosynthetic pigments. Taken together, the results suggest that the blue light-induced female floral sex expression is closely associated with the blue light-induced changes in abscisic acid, auxin, gibberellins, photosynthesis, starch and sucrose metabolism pathways, which is potentially different from the traditional ethylene-dependent pathway.
Morphological Evaluation of Meta-stable Oligomers of α-Synuclein with Small-Angle Neutron Scattering
Authors: Bhak Ghibom , Lee Soonkoo , Kim Tae-Hwan , Lee Ji-Hye , Yang Jee Eun , Joo Keehyoung , Lee Jooyoung , Char Kookheon , Paik Seung R. 
Published: September 2018

AbstractAmyloidogenesis of α-synuclein (αS) is considered to be a pathological phenomenon related to Parkinson’s disease (PD). As a key component to reveal the fibrillation mechanism and toxicity, we have investigated an oligomeric species of αS capable of exhibiting the unit-assembly process leading to accelerated amyloid fibril formation. These oligomers previously shown to exist in a meta-stable state with mostly disordered structure and unable to seed the fibrillation were converted to either temperature-sensitive self-associative oligomers or NaCl-induced non-fibrillating oligomeric species. Despite their transient and disordered nature, the structural information of meta-stable αS oligomers (Meta-αS-Os) was successfully evaluated with small-angle neutron scattering (SANS) technique. By fitting the neutron scattering data with polydisperse Gaussian Coil (pGC) model, Meta-αS-O was analyzed as a sphere with approximate diameter of 100 Å. Its overall shape altered drastically with subtle changes in temperature between 37 °C and 43 °C, which would be responsible for fibrillar polymorphism. Based on their bifurcating property of Meta-αS-Os leading to either on-pathway or off-pathway species, the oligomers could be suggested as a crucial intermediate responsible for the oligomeric diversification and multiple fibrillation processes. Therefore, Meta-αS-Os could be considered as a principal target to control the amyloidogenesis and its pathogenesis.
Occurrence of cagA+ vacA s1a m1 i1 Helicobacter pylori in farm animals in Egypt and ability to survive in experimentally contaminated UHT milk
Authors: Elhariri Mahmoud , Hamza Dalia , Elhelw Rehab , Hamza Eman 
Published: September 2018

AbstractCases of human gastric cancer due to Helicobacter pylori have been reported worldwide and animals might act as a reservoir of infection in certain circumstances. The recent few decades showed a rapid decline in the incidence of gastric cancer, which was mainly due to the decrease in H. pylori infection. The aims of the present study were to determine the prevalence of H. pylori among livestock and investigate whether the animal isolates can be transmitted through contaminated milk causing gastric infection. Feces and milk samples were collected from apparently healthy cows, buffaloes, and sheep, and were examined by nested PCR and genotyping. The PCR positive samples were further subjected to bacterial culture followed by partial 16s sequencing of the isolates. Twenty-nine percent of the animals showed the presence of H. pylori, mainly the virulent cagA+vacA+s1a m1 i1 genotype, which is known to be associated with serious diseases in humans. The spiral viable culturable form (SVCF) of this strain was inoculated into UHT (ultra-high temperature) milk and remained viable for up to 10 days at 4 °C. Increasing period of storage and or temperature led to a decrease in the number of the SVCF and occurrence of the coccoid viable non-culturable form (CVNCF). The infectivity of the survived forms was determined by feeding healthy groups of laboratory mice with the contaminated UHT milk containing SVCF or CVNCF for 40 days. The gastric mucosa of the two mice groups showed similar levels of H. pylori load. This highlights that H. pylori can persist in contaminated milk by entering a non-culturable state, which can induce gastric infection.