bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistent infections with infectious pancreatic necrosis virus (IPNV) of different virulence in Atlantic salmon, Salmo salar L
Authors: Julin K , Johansen L‐H , Sommer A‐I , Jørgensen J B 
Published: December 2014

AbstractInfectious pancreatic necrosis virus (IPNV) is a prevalent pathogen in fish worldwide. The virus causes substantial mortality in Atlantic salmon juveniles and smolts when transferred to sea water and persistent infection in surviving fish after disease outbreaks. Here, we have investigated the occurrence of the virus as well as the innate immune marker Mx in the head kidney (HK) of Atlantic salmon throughout an experimental challenge covering both a fresh and a seawater phase. The fish were challenged with a high (HV) and low virulence (LV) IPNV. Both isolates caused mortality due to reactivation of the virus after transfer to sea water. In the freshwater phase, higher levels of virus transcripts were detected in the HK of fish infected with LV IPNV compared to HV, suggesting that the HV isolate is able to limit its own replication to a level where the innate immune system is not alerted. Further, ex vivoHK leucocytes derived from fish infected with the two isolates were stimulated with CpG DNA. Significantly, higher IFN levels were found in the LV compared to the HV group in the freshwater phase. This suggests that the viruses attenuate the antiviral host immune response at different levels which may contribute to the observed differences in disease outcome.
Background intensity correction for terabyte‐sized time‐lapse images
Authors: CHALFOUN J. , MAJURSKI M. , BHADRIRAJU K. , LUND S. , BAJCSY P. , BRADY M. 
Published: December 2014

SummarySeveral computational challenges associated with large‐scale background image correction of terabyte‐sized fluorescent images are discussed and analysed in this paper. Dark current, flat‐field and background correction models are applied over a mosaic of hundreds of spatially overlapping fields of view (FOVs) taken over the course of several days, during which the background diminishes as cell colonies grow. The motivation of our work comes from the need to quantify the dynamics of OCT‐4 gene expression via a fluorescent reporter in human stem cell colonies. Our approach to background correction is formulated as an optimization problem over two image partitioning schemes and four analytical correction models. The optimization objective function is evaluated in terms of (1) the minimum root mean square (RMS) error remaining after image correction, (2) the maximum signal‐to‐noise ratio (SNR) reached after downsampling and (3) the minimum execution time. Based on the analyses with measured dark current noise and flat‐field images, the most optimal GFP background correction is obtained by using a data partition based on forming a set of submosaic images with a polynomial surface background model. The resulting image after correction is characterized by an RMS of about 8, and an SNR value of a 4 × 4 downsampling above 5 by Rose criterion. The new technique generates an image with half RMS value and double SNR value when compared to an approach that assumes constant background throughout the mosaic. We show that the background noise in terabyte‐sized fluorescent image mosaics can be corrected computationally with the optimized triplet (data partition, model, SNR driven downsampling) such that the total RMS value from background noise does not exceed the magnitude of the measured dark current noise. In this case, the dark current noise serves as a benchmark for the lowest noise level that an imaging system can achieve. In comparison to previous work, the past fluorescent image background correction methods have been designed for single FOV and have not been applied to terabyte‐sized images with large mosaic FOVs, low SNR and diminishing access to background information over time as cell colonies span entirely multiple FOVs. The code is available as open‐source from the following link https://isg.nist.gov/.
Localizing and extracting filament distributions from microscopy images
Authors: BASU S. , LIU C. , ROHDE G.K. 
Published: December 2014

SummaryDetailed quantitative measurements of biological filament networks represent a crucial step in understanding architecture and structure of cells and tissues, which in turn explain important biological events such as wound healing and cancer metastases. Microscopic images of biological specimens marked for different structural proteins constitute an important source for observing and measuring meaningful parameters of biological networks. Unfortunately, current efforts at quantitative estimation of architecture and orientation of biological filament networks from microscopy images are predominantly limited to visual estimation and indirect experimental inference. Here, we describe a new method for localizing and extracting filament distributions from 2D microscopy images of different modalities. The method combines a filter‐based detection of pixels likely to contain a filament with a constrained reverse diffusion‐based approach for localizing the filaments centrelines. We show with qualitative and quantitative experiments, using both simulated and real data, that the new method can provide more accurate centreline estimates of filament in comparison to other approaches currently available. In addition, we show the algorithm is more robust with respect to variations in the initial filter‐based filament detection step often used. We demonstrate the application of the method in extracting quantitative parameters from confocal microscopy images of actin filaments and atomic force microscopy images of DNA fragments.
A novel DYRK1A (Dual specificity tyrosine phosphorylation‐regulated kinase 1A) inhibitor for the treatment of Alzheimer's disease: effect on Tau and amyloid pathologies in vitro
Authors: Coutadeur Séverine , Benyamine Hélène , Delalonde Laurence , de Oliveira Catherine , Leblond Bertrand , Foucourt Alicia , Besson Thierry , Casagrande Anne‐Sophie , Taverne Thierry , Girard Angélique , Pando Matthew P. , Désiré Laurent 
Published: December 2014

AbstractThe dual‐specificity tyrosine phosphorylation‐regulated kinase 1A (DYRK1A) gene is located within the Down Syndrome (DS) critical region on chromosome 21 and is implicated in the generation of Tau and amyloid pathologies that are associated with the early onset Alzheimer's Disease (AD) observed in DS. DYRK1A is also found associated with neurofibrillary tangles in sporadic AD and phosphorylates key AD players (Tau, amyloid precursor, protein, etc). Thus, DYRK1A may be an important therapeutic target to modify the course of Tau and amyloid beta (Aβ) pathologies. Here, we describe EHT 5372 (methyl 9‐(2,4‐dichlorophenylamino) thiazolo[5,4‐f]quinazoline‐2‐carbimidate), a novel, highly potent (IC50 = 0.22 nM) DYRK1A inhibitor with a high degree of selectivity over 339 kinases. Models in which inhibition of DYRK1A by siRNA reduced and DYRK1A over‐expression induced Tau phosphorylation or Aβ production were used. EHT 5372 inhibits DYRK1A‐induced Tau phosphorylation at multiple AD‐relevant sites in biochemical and cellular assays. EHT 5372 also normalizes both Aβ‐induced Tau phosphorylation and DYRK1A‐stimulated Aβ production. DYRK1A is thus as a key element of Aβ‐mediated Tau hyperphosphorylation, which links Tau and amyloid pathologies. EHT 5372 and other compounds in its class warrant in vivo investigation as a novel, high‐potential therapy for AD and other Tau opathies.
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Inhibition of the dual specificity tyrosine‐phosphorylation‐regulated kinase 1A (DYRK1A) is a new high‐potential therapeutic approach for Alzheimer disease. Here we describe EHT 5372, a novel potent and selective DYRK1A inhibitor. EHT 5372 inhibits DYRK1A‐induced Tau phosphorylation, Aβ production and Aβ effects on phospho‐Tau, including Tau aggregation.
Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?
Authors: Alvarez Mariano , Schrey Aaron W. , Richards Christina L. 
Published: December 2014

AbstractMolecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole‐genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.
Recombination of strain O segments to HCpro‐encoding sequence of strain N of Potato virus Y modulates necrosis induced in tobacco and in potatoes carrying resistance genes Ny or Nc
Authors: Tian Yan‐Ping , Valkonen Jari P. T. 
Published: December 2014

SummaryHypersensitive resistance (HR) to strains O and C of Potato virus Y (PVY, genus Potyvirus) is conferred by potato genes Nytbr and Nctbr, respectively; however, PVY N strains overcome these resistance genes. The viral helper component proteinases (HCpro, 456 amino acids) from PVYN and PVYO are distinguished by an eight‐amino‐acid signature sequence, causing HCpro to fold into alternative conformations. Substitution of only two residues (K269R and R270K) of the eight‐amino‐acid signature in PVYN HCpro was needed to convert the three‐dimensional (3D) model of PVYN HCpro to a PVYO‐like conformation and render PVYN avirulent in the presence of Nytbr, whereas four amino acid substitutions were necessary to change PVYO HCpro to a PVYN‐like conformation. Hence, the HCpro conformation rather than other features ascribed to the sequence were essential for recognition by Nytbr. The 3D model of PVYC HCpro closely resembled PVYO, but differed from PVYN HCpro. HCpro of all strains was structurally similar to β‐catenin. Sixteen PVYN605‐based chimeras were inoculated to potato cv. Pentland Crown (Nytbr), King Edward (Nctbr) and Pentland Ivory (Nytbr/Nctbr). Eleven chimeras induced necrotic local lesions and caused no systemic infection, and thus differed from both parental viruses that infected King Edward systemically, and from PVYN605 that infected Pentland Crown and Pentland Ivory systemically. These 11 chimeras triggered both Nytbr and Nctbr and, in addition, six induced veinal necrosis in tobacco. Further, specific amino acid residues were found to have an additive impact on necrosis. These results shed new light on the causes of PVY‐related necrotic symptoms in potato.
Investigation of Aβ phosphorylated at serine 8 (pAβ) in Alzheimer's disease, dementia with Lewy bodies and vascular dementia
Authors: Ashby Emma L. , Miners James S. , Kumar Sathish , Walter Jochen , Love Seth , Kehoe Patrick G. 
Published: December 2014

AimsDeposition of amyloid beta (Aβ) in the brain is one of the defining abnormalities of Alzheimer's disease (AD). Phosphorylation of Aβ at serine 8 (pAβ) has been implicated in its aggregation in vitro and pAβ level has been shown to be significantly elevated in AD. We aimed to assess the specificity of pAβ for AD and have investigated associations of pAβ with parenchymal and cerebrovascular accumulation of Aβ, disease progression, angiotensin‐converting enzyme activity and APOE genotype.MethodsThe distribution of pAβ was studied by immunohistochemistry in sporadic and familial AD, pure dementia with Lewy bodies (DLB), pure vascular dementia (VaD) and age‐matched controls. Soluble and insoluble (guanidine‐extractable) pAβ level was measured by enzyme‐linked immunosorbent assay (ELISA) in the midfrontal and parahippocampal cortex in sporadic AD (n = 20, 10 with Braak tangle stages of III–IV and 10 of stages V–VI), DLB (n = 10), VaD (n = 10) and age‐matched controls (n = 20).ResultsWe found pAβ to be associated with only a subset of Aβ plaques and vascular deposits in sporadic and familial AD, with absent or minimal immunohistochemically detectable pAβ in control, DLB and VaD brains. In both brain regions, insoluble pAβ level was significantly elevated only in advanced AD (Braak tangle stage of V or VI) and in the parahippocampus soluble and insoluble pAβ level increased with the number of APOE ε4 alleles.ConclusionsThese results indicate that pAβ accumulation in the parenchyma and vasculature is largely restricted to late‐stage AD (Braak tangle stage V–VI).
Analysis of phenotypic change in relation to climatic drivers in a population of Soay sheep Ovis aries
Authors: Simmonds Emily G. , Coulson Tim 
Published: December 2014

Climatic change has frequently been identified as a key driver of change in biological communities. These changes can take the form of alterations to population dynamics, phenotypic characters, genetics and the life history of organisms and can have impacts on entire ecosystems. This study presents a novel investigation of how changes in a large scale climatic index, the North Atlantic Oscillation (NAO) can influence population dynamics and phenotypic characters in a population of ungulates. We use an integral projection model combined with actual climate change predictions to project future body size distributions for a population of Soay sheep Ovis aries. The climate change predictions used to direct our model projections were taken from published results of climate models, covering a range of different emissions scenarios. Our model results showed that for positive changes in the mean NAO large population declines occurred simultaneously with increases in mean body weight. The exact direction and magnitude of changes to population dynamics and character distributions were dependent on the greenhouse gas emissions scenario and model used to predict the NAO. This study has demonstrated how integral projection models can use outputs of climate models to direct projections of population dynamics and phenotypic character distributions. This approach allows the results of this study to be placed within current climate change research. The nature of integral projection models means that this methodology can be easily applied to other populations. The model can also be easily updated when new climate change predictions become available, making it a useful tool for understanding potential population level responses to climatic change.SynthesisUnderstanding how changes in climate affect biological communities is a key component in predicting the future form of populations. Utilising a novel approach that incorporates climatic drivers (in this instance the winter North Atlantic Oscillation) into an integral projection model framework, we predict future Soay sheep dynamics under specific climate change scenarios. Tracking quantitative trait distributions and life history metrics, our results predict declining population size and increasing body weight for an increasingly positive winter North Atlantic Oscillation index, as predicted by climate models. This has important implications for future wildlife management strategies and linking demographic responses to climate change.
Rhinitis in the first 18 months of life: Exploring the role of respiratory viruses
Authors: Hardjojo Antony , Goh Anne , Shek Lynette P.C. , Van Bever Hugo P. S. , Teoh Oon Hoe , Soh Jian Yi , Thomas Biju , Tan Boon Huan , Chan Yiong Huak , Ramamurthy Mahesh Babu , Goh Daniel Y. T. , Soh Shu‐E , Saw Seang‐Mei , Kwek Kenneth , Chong Yap‐Seng , Godfrey Keith M. , Gluckman Peter D. , Lee Bee Wah 
Published: December 2014

AbstractBackgroundRhinitis is common in early childhood, but allergic rhinitis is considered a later manifestation of the atopic march. This study aimed to evaluate rhinitis (allergic and non‐allergic) in the first 18 months of life, its link with other atopic manifestations and the role of respiratory viruses.MethodsSubjects (n = 1237) of the Singapore GUSTO birth cohort were followed up quarterly until 18 months of age with questionnaires to screen for rhinitis symptoms lasting at least 2 wk and with monthly calls to positive subjects to detect prolonged/recurrent rhinitis symptoms (total duration ≥4 wk). Anterior nasal swabbing for molecular‐based virus detection was conducted during these visits and near (within a month) rhinitis episodes. Skin prick testing to common environmental and food allergens was conducted at the 18 month visit.ResultsProlonged/recurrent rhinitis was significantly associated with history of parental atopy (mother: aOR = 2.17; father: aOR = 1.82) and atopic comorbidities of eczema (aOR = 2.53) and wheeze (aOR = 4.63) (p < 0.05), though not with allergen sensitization. Although the frequency of nasal respiratory virus detection during scheduled quarterly visits did not differ between prolonged/recurrent rhinitis and matched controls (p > 0.05), virus detection was higher in swabs obtained within a month following rhinitis episodes in prolonged/recurrent rhinitis subjects compared with scheduled visits (adjusted p = 0.04).ConclusionsBased on the duration of rhinitis symptoms, this study defined a subset of early childhood rhinitis which was associated with atopic predisposition and comorbidities. Persistent respiratory viral shedding may contribute to the symptomatology. Whether this entity is a precursor of subsequent childhood allergic rhinitis will require longer follow‐up.
Overexpression of patatin‐related phospholipase AIIIδ altered plant growth and increased seed oil content in camelina
Authors: Li Maoyin , Wei Fang , Tawfall Amanda , Tang Michelle , Saettele Allison , Wang Xuemin 
Published: December 2014

SummaryCamelina sativa is a Brassicaceae oilseed species being explored as a biofuel and industrial oil crop. A growing number of studies have indicated that the turnover of phosphatidylcholine plays an important role in the synthesis and modification of triacylglycerols. This study manipulated the expression of a patatin‐related phospholipase AIIIδ (pPLAIIIδ) in camelina to determine its effect on seed oil content and plant growth. Constitutive overexpression of pPLAIIIδ under the control of the constitutive cauliflower mosaic 35S promoter resulted in a significant increase in seed oil content and a decrease in cellulose content. In addition, the content of major membrane phospholipids, phosphatidylcholine and phosphatidylethanolamine, in 35S::pPLAIIIδ plants was increased. However, these changes in 35S::pPLAIIIδ camelina were associated with shorter cell length, leaves, stems, and seed pods and a decrease in overall seed production. When pPLAIIIδ was expressed under the control of the seed specific, β‐conglycinin promoter, the seed oil content was increased without compromising plant growth. The results suggest that pPLAIIIδ alters the carbon partitioning by decreasing cellulose content and increasing oil content in camelina.
Outpatient Use of Oral Propranolol and Topical Timolol for Infantile Hemangiomas: Survey Results and Comparison with Propranolol Consensus Statement Guidelines
Authors: Kumar Monique G. , Coughlin Carrie , Bayliss Susan J. 
Published: December 2014

AbstractOral and topical β‐blockers are used to treat infantile hemangiomas (IHs). Although a recent consensus report provided guidelines for the treatment of IH with propranolol, there are no standard guidelines for the use of topical timolol. The objectives of this study were to determine the current use of oral propranolol and topical timolol by pediatric dermatologists in an outpatient setting and to compare current propranolol use with published propranolol consensus guidelines. An electronic survey was sent to pediatric dermatologists in May and June 2013. One hundred forty‐nine pediatric dermatologists responded to the survey, a 79% response rate. Of the respondents, 96% prescribed oral propranolol, but 75% did not follow consensus guidelines exactly; recommended history, physical examination, initial dose, and frequency varied. The dose of propranolol was usually titrated up to goal dose as recommended (89%). Fifty‐six percent monitored vital signs in patients after the initial dose and 49% continued to monitor vital signs in their clinic after each dose escalation, which did not meet consensus guideline recommendations. Ninety‐one percent reported using topical timolol for the treatment of IH and 66% responded they had used topical timolol in conjunction with oral propranolol to treat IH. The most common indication was superficial hemangiomas (97%). Most practitioners (74%) did not routinely monitor heart rate or blood pressure in infants treated with topical timolol. This study highlights the variability in prescribing and monitoring practices of physicians using propranolol for the treatment of IHs and demonstrates that topical timolol is commonly used alone and in conjunction with oral propranolol to treat IHs.
Thread Epilation: A Less Traumatic Technique for Patients Undergoing Isotretinoin Therapy
Authors: Wu Sam , Bhandari Rachna , Burkhart Craig N. 
Published: December 2014

AbstractSkin fragility is a well‐established complication of isotretinoin therapy for severe or resistant acne and presents a challenge to traditional modes of epilation such as waxing. As such, other less traumatic hair removal methods are desired. Herein we present the threading technique as an alternative form of epilation for patients in whom waxing is contraindicated secondary to concerns over skin fragility.
Nevus Comedonicus: A Case Series
Authors: Ferrari Bruno , Taliercio Vanina , Restrepo Paola , Luna Paula , Abad María Eugenia , Larralde Margarita 
Published: December 2014

AbstractTwelve previously unreported cases of nevus comedonicus are presented. Characteristic closely grouped dilated follicular openings with horny plugs that mimic comedones led to the diagnosis. One patient had nevus comedonicus syndrome and there were cases with atypical locations and unusual complications of this condition. We also highlight clinical associations and therapeutic options.
Successful Treatment of Pearly Penile Papules with Carbon Dioxide Laser Resurfacing After Local Anesthesia in an Adolescent Patient
Authors: Krakowski Andrew C. , Feldstein Stephanie , Shumaker Peter R. 
Published: December 2014

AbstractPearly penile papules (PPP) can cause significant psychological morbidity. Herein we report the successful use of a macrofractionated carbon dioxide laser at full‐field ablative density settings for the treatment of PPP in a 17‐year‐old boy using local anesthetic alone. Our experience leads us to believe that PPP can be successfully treated in the pediatric and adolescent populations using this novel and relatively noninvasive technique.