bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the β-defensin genes in giant panda
Authors: Zhang Zhi-Yi , Zhang He-Min , Li De-Sheng , Xiong Tie-Yi , Fang Sheng-Guo 
Published: August 2018

Abstractβ-Defensins are small antimicrobial proteins expressed in various organisms and have great potential for improving animal health and selective breeding programs. Giant pandas have a distinctive lineage in Carnivora, and it is unclear whether β-defensin genes have experienced different selective pressures during giant panda evolution. We therefore characterized the giant panda (Ailuropoda melanoleuca) β-defensin gene family through gap filling, TBLASTN, and HMM searches. Among 36 β-defensins identified, gastrointestinal disease may induce the expression of theDEFB1andDEFB139genes in the digestive system. Moreover, forDEFB139, a significant positive selection different from that of its homologs was revealed through branch model comparisons. A Pro-to-Arg mutation in the giant panda DEFB139 mature peptide may have enhanced the peptide’s antimicrobial potency by increasing its stability, isoelectric point, surface charge and surface hydrophobicity, and by stabilizing its second β-sheet. Broth microdilution tests showed that the increase in net charge caused by the Pro-to-Arg mutation has enhanced the peptide’s potency againstStaphylococcus aureus, although the increase was minor. We expect that additional gene function and expression studies of the giant pandaDEFB139gene could improve the existing conservation strategies for the giant panda.
Predictive ability of genome-assisted statistical models under various forms of gene action
Authors: Momen Mehdi , Mehrgardi Ahmad Ayatollahi , Sheikhi Ayyub , Kranis Andreas , Tusell Llibertat , Morota Gota , Rosa Guilherme J. M. , Gianola Daniel 
Published: August 2018

AbstractRecent work has suggested that the performance of prediction models for complex traits may depend on the architecture of the target traits. Here we compared several prediction models with respect to their ability of predicting phenotypes under various statistical architectures of gene action: (1) purely additive, (2) additive and dominance, (3) additive, dominance, and two-locus epistasis, and (4) purely epistatic settings. Simulation and a real chicken dataset were used. Fourteen prediction models were compared: BayesA, BayesB, BayesC, Bayesian LASSO, Bayesian ridge regression, elastic net, genomic best linear unbiased prediction, a Gaussian process, LASSO, random forests, reproducing kernel Hilbert spaces regression, ridge regression (best linear unbiased prediction), relevance vector machines, and support vector machines. When the trait was under additive gene action, the parametric prediction models outperformed non-parametric ones. Conversely, when the trait was under epistatic gene action, the non-parametric prediction models provided more accurate predictions. Thus, prediction models must be selected according to the most probably underlying architecture of traits. In the chicken dataset examined, most models had similar prediction performance. Our results corroborate the view that there is no universally best prediction models, and that the development of robust prediction models is an important research objective.
Immuno-impedimetric Biosensor for Onsite Monitoring of Ascospores and Forecasting of Sclerotinia Stem Rot of Canola
Authors: Shoute Lian C. T. , Anwar Afreen , MacKay Scott , Abdelrasoul Gaser N. , Lin Donghai , Yan Zhimin , Nguyen Anh H. , McDermott Mark T. , Shah Manzoor A. , Yang Jian , Chen Jie , Li Xiujie S. 
Published: August 2018

AbstractSclerotinia stem rot, caused by the fungal pathogen Sclerotinia sclerotiorum, is a destructive disease of canola and many other broadleaf crops. The primary inoculum responsible for initiating Sclerotinia epidemics is airborne ascospores released from the apothecia of sclerotia. Timely detection of the presence of airborne ascospores can serve as an early-warning system for forecasting and management of the disease. A major challenge is to develop a portable and automated device which can be deployed onsite to detect and quantify the presence of minute quantities of ascospores in the air and serves as a unit in a network of systems for forecasting of the epidemic. In this communication, we present the development of an impedimetric non-Faradaic biosensor based on anti-S. sclerotiorum polyclonal antibodies as probes to selectively capture the ascospores and sense their binding by an impedance based interdigitated electrode which was found to directly and unambiguously correlate the number of ascospores on sensor surface with the impedance response.
Improving precision for detecting change in the shape of the cornea in patients with keratoconus
Authors: Brunner Matthias , Czanner Gabriela , Vinciguerra Riccardo , Romano Vito , Ahmad Sajjad , Batterbury Mark , Britten Claire , Willoughby Colin E. , Kaye Stephen B. 
Published: August 2018

AbstractTo investigate a method for precision analysis to discriminate true corneal change from measurement imprecision in keratoconus (KC). Thirty patients with KC and 30 healthy controls were included. Coefficients of repeatability and limits of agreement (LOA) were compared using multiple measurements for inter-observer and inter-device agreement with the Pentacam HR, Orbscan IIz, and Tomey Casia SS-1000. Correlation of repeated measurements was evaluated using a linear mixed effect model (also called random effect model). A formula was derived for the theoretical expected change in precision and compared with measured change. Correlation between measurements from the same eye was small (R = 0.13). The 99.73% LOA (3 SD) of the mean of three measurements, provided better precision than 95% LOA (2 SD) of single cut-off values as expected from statistical theory for uncorrelated measurements for evidence of a significant change in corneal shape in patients with keratoconus. This enabled the determination of cut-off values for the detection of true change in corneal shape. The mean of three repeated measurements will provide better precision when there is minimal correlation. Three (rather than two) standard deviations provides a precise estimate of the LOA within or between observers and can be used as a reliable measure for identifying stage-independent corneal shape changes (progression) in keratoconus.
Membrane-Modulating Drugs can Affect the Size of Amyloid-β25–35 Aggregates in Anionic Membranes
Authors: Khondker Adree , Alsop Richard J. , Himbert Sebastian , Tang Jennifer , Shi An-Chang , Hitchcock Adam P. , Rheinstädter Maikel C. 
Published: August 2018

AbstractThe formation of amyloid-βplaques is one of the hallmarks of Alzheimer’s disease. The presence of an amphiphatic cell membrane can accelerate the formation of amyloid-βaggregates, making it a potential druggable target to delay the progression of Alzheimer’s disease. We have prepared unsaturated anionic membranes made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine (DMPS) and added the trans-membrane segment Aβ25–35. Peptide plaques spontaneously form in these membranes at high peptide concentrations of 20 mol%, which show the characteristic cross-βmotif (concentrations are relative to the number of membrane lipids and indicate the peptide-to-lipid ratio). We used atomic force microscopy, fluorescence microscopy, x-ray microscopy, x-ray diffraction, UV-vis spectroscopy and Molecular Dynamics (MD) simulations to study three membrane-active molecules which have been speculated to have an effect in Alzheimer’s disease: melatonin, acetylsalicyclic acid (ASA) and curcumin at concentrations of 5 mol% (drug-to-peptide ratio). Melatonin did not change the structural parameters of the membranes and did not impact the size or extent of peptide clusters. While ASA led to a membrane thickening and stiffening, curcumin made membranes softer and thinner. As a result, ASA was found to lead to the formation of larger peptide aggregates, whereas curcumin reduced the volume fraction of cross-βsheets by ~70%. We speculate that the interface between membrane and peptide cluster becomes less favorable in thick and stiff membranes, which favors the formation of larger aggregates, while the corresponding energy mismatch is reduced in soft and thin membranes. Our results present evidence that cross-βsheets of Aβ25–35in anionic unsaturated lipid membranes can be re-dissolved by changing membrane properties to reduce domain mismatch.
An Evaluation of the Collagen Fragments Related to Fibrogenesis and Fibrolysis in Nonalcoholic Steatohepatitis
Authors: Luo Yi , Oseini Abdul , Gagnon Robert , Charles Edgar D. , Sidik Kurex , Vincent Robert , Collen Rebeca , Idowu Michael , Contos Melissa J. , Mirshahi Faridoddin , Daita Kalyani , Asgharpour Amon , Siddiqui Mohammed S. , Jarai Gabor , Rosen Glenn , Christian Rose , Sanyal Arun J. 
Published: August 2018

AbstractFibrosis, resulted from the imbalance of fibrogenesis and fibrolysis, is a key readout of disease progression in nonalcoholic steatohepatitis (NASH) and reflects mortality risk. Non-invasive biomarkers capable of diagnosing fibrosis stages and monitoring fibrosis changes in NASH patients are urgently needed. This study is to evaluate collagen formation and degradation biomarkers, reflective of fibrogenesis or fibrolysis, in patients with biopsy proven NASH. Collagen formation biomarker PRO-C3 and PRO-C6 levels were significantly higher in patients with advanced fibrosis stage 3–4 than those with fibrosis stage 0–2. Elevated PRO-C3 levels were also associated with severe lobular inflammation and ballooning, but not with steatosis. Multivariate logistic regression analysis identified PRO-C3 and PRO-C6 to be independently related to fibrosis stage. PRO-C3 showed similar performance to identify patients with advanced fibrosis in discovery and validation cohorts. Furthermore, in a longitudinal study cohort with paired biopsies, mean PRO-C3 increased with worsening of fibrosis and decreased with fibrosis improvement. The results suggest that PRO-C3 may be a potentially useful biomarker in identifying patients with advanced fibrosis and active fibrogenesis, as well as in assessing changes in fibrosis over time. It is worthy of further evaluation to confirm its diagnostic value and clinical utility.
A 2′FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein
Authors: Shubham Shambhavi , Hoinka Jan , Banerjee Soma , Swanson Emma , Dillard Jacob A. , Lennemann Nicholas J. , Przytycka Teresa M. , Maury Wendy , Nilsen-Hamilton Marit 
Published: August 2018

AbstractWith properties such as stability to long-term storage and amenability to repetitive use, nucleic acid aptamers are compatible with many sensing/transducing platforms intended for use in remote locations. Sensors with these properties are important for quickly identifying ebolavirus outbreaks, which frequently start in locations that lack sophisticated equipment. Soluble glycoprotein (sGP), an excellent biomarker for ebolaviruses, is produced from the same gene as the ebolavirus glycoprotein GP1,2 that decorates the surface of the viral particle and is secreted in abundance into the blood stream even during the early stages of infection. Here, we report the selection and properties of a 2′fluoro pyrimidine (2′FY)-modified RNA aptamer, 39SGP1A, that specifically binds sGP. We demonstrate by computational and biochemical analysis that the recognition motif of 39SGP1A is a novel polypyrimidine-rich sequence. Replacement of -F by -OH in the 2′ position of the ribose resulted in complete loss of affinity for sGP. The protein motif to which the aptamer binds requires an intact sGP dimer and binds to an epitope conserved between Ebola virus (EBOV) and Sudan virus (SUDV) sGP, the most divergent Ebolavirus species. This identifies 39SGP1A as an excellent option for integration on a sensor platform to detect ebolavirus infections.
Genome-wide Association Analysis of Eye Movement Dysfunction in Schizophrenia
Authors: Kikuchi Masataka , Miura Kenichiro , Morita Kentaro , Yamamori Hidenaga , Fujimoto Michiko , Ikeda Masashi , Yasuda Yuka , Nakaya Akihiro , Hashimoto Ryota 
Published: August 2018

AbstractEye movements are considered endophenotypes of schizophrenia. However, the genetic factors underlying eye movement are largely unknown. In this study, we explored the susceptibility loci for four eye movement scores: the scanpath length during the free viewing test (SPL), the horizontal position gain during the fast Lissajous paradigm of the smooth pursuit test (HPG), the duration of fixations during the far distractor paradigm of the fixation stability test (DF) and the integrated eye movement score of those three scores (EMS). We found 16 SNPs relevant to the HPG that were located in 3 genomic regions (1q21.3, 7p12.1 and 20q13.12) in the patient group; however, these SNPs were intronic or intergenic SNPs. To determine whether these SNPs occur in functional non-coding regions (i.e., enhancer or promoter regions), we examined the chromatin status on the basis of publicly available epigenomic data from 127 tissues or cell lines. This analysis suggested that the SNPs on 1q21.3 and 20q13.12 are in enhancer or promoter regions. Moreover, we performed an analysis of expression quantitative trait loci (eQTL) in human brain tissues using a public database. Finally, we identified significant eQTL effects for all of the SNPs at 1q21.3 and 20q13.12 in particular brain regions.
Zero-shot fMRI decoding with three-dimensional registration based on diffusion tensor imaging
Authors: Fuchigami Takuya , Shikauchi Yumi , Nakae Ken , Shikauchi Manabu , Ogawa Takeshi , Ishii Shin 
Published: August 2018

AbstractFunctional magnetic resonance imaging (fMRI) acquisitions include a great deal of individual variability. This individuality often generates obstacles to the efficient use of databanks from multiple subjects. Although recent studies have suggested that inter-regional connectivity reflects individuality, conventional three-dimensional (3D) registration methods that calibrate inter-subject variability are based on anatomical information about the gray matter shape (e.g., T1-weighted). Here, we present a new registration method focusing more on the white matter structure, which is directly related to the connectivity in the brain, and apply it to subject-transfer brain decoding. Our registration method based on diffusion tensor imaging (DTI) transferred functional maps of each individual to a common anatomical space, where a decoding analysis of multi-voxel patterns was performed. The decoder trained on functional maps from other individuals in the common space showed a transfer decoding accuracy comparable to that of an individual decoder trained on single-subject functional maps. The DTI-based registration allowed more precise transformation of gray matter boundaries than a well-established T1-based method. These results suggest that the DTI-based registration is a promising tool for standardization of the brain functions, and moreover, will allow us to perform ‘zero-shot’ learning of decoders which is profitable in brain machine interface scenes.
Phospholipidome of endothelial cells shows a different adaptation response upon oxidative, glycative and lipoxidative stress
Authors: Colombo Simone , Melo Tânia , Martínez-López Marta , Carrasco M. Jesús , Domingues M. Rosário , Pérez-Sala Dolores , Domingues Pedro 
Published: August 2018

AbstractEndothelial dysfunction has been widely associated with oxidative stress, glucotoxicity and lipotoxicity and underlies the development of cardiovascular diseases (CVDs), atherosclerosis and diabetes. In such pathological conditions, lipids are emerging as mediators of signalling pathways evoking key cellular responses as expression of proinflammatory genes, proliferation and apoptosis. Hence, the assessment of lipid profiles in endothelial cells (EC) can provide valuable information on the molecular alterations underlying CVDs, atherosclerosis and diabetes. We performed a lipidomic approach based on hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) for the analysis of the phospholipidome of bovine aortic EC (BAEC) exposed to oxidative (H2O2), glycative (glucose), or lipoxidative (4-hydroxynonenal, HNE) stress. The phospholipid (PL) profile was evaluated for the classes PC, PE, PS, PG, PI, SM, LPC and CL. H2O2 induced a more acute adaptation of the PL profile than glucose or HNE. Unsaturated PL molecular species were up-regulated after 24 h incubation with H2O2, while an opposite trend was observed in glucose- and HNE-treated cells. This study compared, for the first time, the adaptation of the phospholipidome of BAEC upon different induced biochemical stresses. Although further biological studies will be necessary, our results unveil specific lipid signatures in response to characteristic types of stress.
Olea europaea small RNA with functional homology to human miR34a in cross-kingdom interaction of anti-tumoral response
Authors: Minutolo Antonella , Potestà Marina , Gismondi Angelo , Pirrò Stefano , Cirilli Marco , Gattabria Fabiano , Galgani Andrea , Sessa Libera , Mattei Maurizio , Canini Antonella , Muleo Rosario , Colizzi Vittorio , Montesano Carla 
Published: August 2018

AbstractFunctional foods include compounds with nutritional and health properties. The human diet could play a stronger role in cancer prevention. Only a few studies have described the presence of plant small RNA, in humans who were fed with plant foods, which demonstrated the ability of these molecules to modulate consumer’s genes and evidenced the existence of a plant-animal regulation. Through in silico prediction, Olea europaea small RNAs (sRs), which had been previously reported as miRNAs, were identified, each with functional homology to hsa-miR34a. According to this initial funding, we investigated the ability of oeu-sRs to regulate tumorigenesis in human cells. The transfection of these synthetic oeu-sRs reduced the protein expression of hsa-miR34a mRNA targets, increased apoptosis and decreased proliferation in different tumor cells; by contrast, no effect was observed in PBMCs from healthy donors. The introduction of oeu-small RNA in hsa-miR34a-deficient tumor cells restores its function, whereas cells with normal expression of endogenous hsa-miR34a remained unaffected. The natural oeu-small RNAs that were extracted from O. europaea drupes induce the same effects as synthetic sRs. Careful research on the small RNA sequences executed for mapping and annotation in the genome of O. europaea var. Sylvestris and var. Farga led to the hypothesis that RNA fragments with functional homology to human miRNAs could be generated from the degradation of regions of RNA transcripts. These results indicate the possibility of developing novel natural non-toxic drugs that contain active plant-derived tumor-suppressing small RNA with functional homology to hsa-miRNAs and that can support antineoplastic strategies.
Multicilin and activated E2f4 induce multiciliated cell differentiation in primary fibroblasts
Authors: Kim Seongjae , Ma Lina , Shokhirev Maxim N. , Quigley Ian , Kintner Chris 
Published: August 2018

AbstractMulticiliated cells (MCCs) are specialized epithelial cells that project hundreds of motile cilia. To form these cilia, MCCs differentiate by dramatically expanding centriole number, using assembly factors required for centriole duplication during the cell cycle and multiple, novel assembly sites, called the deuterosome. The small coiled-coil protein, Multicilin, acting in a complex with the E2F proteins can initiate multiciliated cell differentiation, but reportedly only in a limited range of epithelial progenitors. To examine the nature of this restricted activity, we analyzed Multicilin activity in primary mouse embryonic fibroblasts (MEFs), a cell type distant from the epithelial lineages where MCCs normally arise. We show that Multicilin transcriptional activity is markedly attenuated in MEFs, where it induces only limited centriole expansion in a small fraction of cells. We further show that this transcriptional block is largely bypassed by expressing Multicilin along with a form of E2f4 where a generic activation domain from HSV1 VP16 (E2f4VP16) is fused to the carboxy terminus. MEFs respond to Multicilin and E2f4VP16 by undergoing massive centriole expansion via the deuterosome pathway, recapitulating a temporal sequence of organelle biogenesis that occurs in epithelial progenitors during MCC differentiation. These results suggest that the pattern of organelle biogenesis occurring in differentiating MCCs is largely determined by the transcriptional changes induced by Multicilin.
Evaluation of the diagnostic accuracy of Computer-Aided Detection of tuberculosis on Chest radiography among private sector patients in Pakistan
Authors: Zaidi Syed Mohammad Asad , Habib Shifa Salman , Van Ginneken Bram , Ferrand Rashida Abbas , Creswell Jacob , Khowaja Saira , Khan Aamir 
Published: August 2018

AbstractThe introduction of digital CXR with automated computer-aided interpretation, has given impetus to the role of CXR in TB screening, particularly in low resource, high-burden settings. The aim of this study was to evaluate the diagnostic accuracy of CAD4TB as a screening tool, implemented in the private sector in Karachi, Pakistan. This study analyzed retrospective data from CAD4TB and Xpert MTB/RIF testing carried out at two private TB treatment and diagnostic centers in Karachi. Sensitivity, specificity, potential Xperts saved, were computed and the receiver operator characteristic curves were constructed for four different models of CAD4TB. A total of 6,845 individuals with presumptive TB were enrolled in the study, 15.2% of which had MTB + ve result on Xpert. A high sensitivity (range 65.8–97.3%) and NPV (range 93.1–98.4%) were recorded for CAD4TB. The Area under the ROC curve (AUC) for CAD4TB was 0.79. CAD4TB with patient demographics (age and gender) gave an AUC of 0.83. CAD4TB offered high diagnostic accuracy. In low resource settings, CAD4TB, as a triage tool could minimize use of Xpert. Using CAD4TB in combination with age and gender data enhanced the performance of the software. Variations in demographic information generate different individual risk probabilities for the same CAD4TB scores.
Alberta wildfire 2016: Apt contribution from anomalous planetary wave dynamics
Authors: Petoukhov Vladimir , Petri Stefan , Kornhuber Kai , Thonicke Kirsten , Coumou Dim , Schellnhuber Hans Joachim 
Published: August 2018

AbstractIn May-June 2016 the Canadian Province of Alberta suffered one of the most devastating wildfires in its history. Here we show that in mid-April to early May 2016 the large-scale circulation in the mid- and high troposphere of the middle and sub-polar latitudes of the northern hemisphere featured a persistent high-amplitude planetary wave structure dominated by the non-dimensional zonal wave number 4. The strongest anticyclonic wing of this structure was located over western Canada. In combination with a very strong El Niño event in winter 2015/2016 this favored highly anomalous, tinder-dry and high-temperature conditions at the surface in that area, entailing an increased fire hazard there. This critically contributed to the ignition of the Alberta Wildfire in May 2016, appearing to be the costliest disaster in Canadian history thus far.