bluuebunny/crossref_metadata_2025_split huggingface dataset:
TCRβ repertoire of memory T cell reveals potential role for Escherichia coli in the pathogenesis of primary biliary cholangitis
Authors: Hou Xianliang , Yang Yida , Chen Jianing , Jia Hongyu , Zeng Ping , Lv Longxian , Lu Yingfeng , Liu Xiangdong , Diao Hongyan 
Published: February 2019

AbstractBackgroundPrimary biliary cholangitis (PBC) is an organ‐specific, T cell‐mediated autoimmune disease which is characterized by the breakdown of self‐tolerance to the highly conserved pyruvate dehydrogenase complex, especially the pyruvate dehydrogenase E2 complex (PDC‐E2). However, the molecular mechanism of breakdown of self‐tolerance is still unclear.MethodsA combination of multiplex‐PCR and immune repertoire sequencing (IR‐seq) was used for a standardized analysis of memory T cell receptor (TCR) β‐chain repertoire of PBC patient and healthy volunteers. In vitro induction and expansion of human PDC‐E2163‐176 (human PDC‐E2)‐specific T cells and E coli PDC‐E231‐44/134‐147/235‐248 (E coli PDC‐E2)‐specific T cells, and identified the human (and E coli) PDC‐E2‐specific TCRβ repertoire by IR‐seq.ResultsPrimary biliary cholangitis patients have shorter complementarity‐determining region 3s (CDR3s), and higher degree of sequence overlap in the TCRβ repertoire of memory T cell. Moreover, altered insertion patterns and skewed TRBV segment usage were observed in PBC patients. With regard to the pathogenesis, the concentration of E coli was higher in PBC patients’ faecal. The frequency of E coli (and human)‐specific TCRs was higher in the memory TCRβ repertoire of PBC patients compared with healthy controls. Importantly, the TCRβ repertoire characteristics were almost identical between E coli PDC‐E2‐related TCRs and human PDC‐E2‐related TCRs, including the patterns of TRBV usage, CDR3 length and amino acid composition.ConclusionOur findings comprehensively revealed the TCRβ repertoire characterization of PBC patients, and provided a TCR molecular basis to understand the mechanism of cross‐recognition between human PDC‐E2 and E coli PDC‐E2, and the imbalance of immune tolerance in PBC.
Effects of moisture dynamics on bryophyte carbon fluxes in a tropical cloud forest
Authors: Metcalfe Daniel B. , Ahlstrand Jenny C. M. 
Published: February 2019

Summary

Bryophytes play key roles in the ecological function of a number of major world biomes but remain understudied compared with vascular plants. Little is known about bryophyte responses to different aspects of predicted changes in moisture dynamics with climate change.

In this study, CO2 fluxes and photosynthetic light responses were measured within bryophyte mesocosms, being subjected to different amounts, frequencies, and types (mist or rainfall) of water addition, both before and after different periods of complete desiccation.

Bryophyte carbon fluxes and photosynthetic light response were generally affected by the magnitude and type, but not frequency, of watering events. Desiccation suppressed bryophyte carbon uptake even after rehydration, and the degree of uptake suppression progressively increased with desiccation duration. Estimated ecosystem‐level bryophyte respiration and net carbon uptake were c. 58% and c. 3%, respectively, of corresponding fluxes from tree foliage at the site.

Our results suggest that a simplified representation of precipitation processes may be sufficient to accurately model bryophyte carbon cycling under future climate scenarios. Further, we find that projected increases in drought could have strong negative impacts on bryophyte and ecosystem carbon storage, with major consequences for a wide range of ecosystem processes.
Patient‐derived xenografts of a case of ameloblastic fibrodentinoma
Authors: Pereira Núbia B. , de Souza Juliana C. , Bastos Victor C. , Fonseca Felipe P. , de Avelar Gleide F. , Castro Wagner H. , Dias Adriana A. M. , Mosqueda‐Taylor Adalberto , Gomez Ricardo S. , Gomes Carolina C. 
Published: February 2019

AbstractObjectivesThe establishment of animal models of xenotransplantation can contribute to the elucidation of the molecular pathogenesis of ameloblastic fibrodentinomas (AFD) and it also provides an opportunity for drug tests. We aimed to evaluate the possibility of AFD tumour growth in a patient‐derived xenograft (PDX) model. In addition, we characterized the human tumour and the PDXs.Materials and MethodsA sample of a recurrent AFD was obtained and two fragments were contralaterally implanted subcutaneously in an 8‐week old female NUDE mouse. After 250 days, the PDXs were removed and submitted to histopathological and molecular analysis. Immunohistochemical reactions for Ki67 and the phosphorylated form of ERK1/2 were carried out in both, PDXs and human tumour, and the presence of BRAFV600E was assessed.ResultsFrom day 135 onwards, the PDXs presented a growth peak and remained stable until day 250. Histopathologically, the PDXs presented the same features of the patient’s tumour. Tumour cells exhibited Ki67 and pERK1/2 immunoexpression in the patient’s tumour and PDX. The AFD was wild‐type for BRAFV600E.ConclusionThe PDX model recapitulated well the human tumour after a long implantation time, representing a possible model to study the AFD and other odontogenic tumours pathobiology.
High mobility group box 1 and markers of oxidative stress in human cord blood
Authors: D'Angelo Gabriella , Granese Roberta , Marseglia Lucia , Impellizzeri Pietro , Alibrandi Angela , Palmara Antonella , La Rosa Maria Angela , Manti Sara , Salpietro Carmelo , Spina Edoardo , Reiter Russel J , Falsaperla Raffaele , Corsello Giovanni , Gitto Eloisa 
Published: February 2019

AbstractBackgroundParturition induces considerable oxidative stress and many inflammatory mediators, such as high mobility group box 1 (HMGB1), are involved from the beginning of the pregnancy to birth. The aim of the present study was to evaluate serum cord blood concentration of diacron‐reactive oxygen metabolites (d‐ROM), biological antioxidant potential (BAP), and HMGB1 to investigate the perinatal oxidative status of neonates and correlation with mode of delivery, as well as the influence of labor.MethodsThe subjects consisted of 214 neonates delivered at University Hospital “G. Martino”, Messina, in a 6 months period. Venous blood samples were collected from the umbilical cord after cord separation.ResultsUmbilical cord venous blood HMGB1 was significantly higher in the spontaneous vaginal delivery (SVD) group than in the elective or emergency cesarean section (CS) group (P = 0.018). Regarding labor, there was no significant difference in HMGB1 concentration in umbilical vein blood between the spontaneous and induced labor groups (P = 0.250). Furthermore, d‐ROM was significantly different between the SVD group and the elective or emergency CS group (P = 0.044). BAP concentration, however, was not significantly different, not even with regard to mode of labor.ConclusionOxidation is higher in newborns delivered by SVD than in those delivered by CS, and HMGB1 may be involved in the mechanisms of birth, and responsible for decidual modifications that lead to birth.
Detection of ‘Candidatus Liberibacter asiaticus’ in citrus by concurrent tissue print‐based qPCR and immunoassay
Authors: Fu S. M. , Liu H. W. , Liu Q. H. , Zhou C. Y. , Hartung J. S. 
Published: February 2019

‘Candidatus Liberibacter asiaticus’ (CLas) is associated with the most destructive disease of citrus, huanglongbing (HLB). The most widely used methods for detection of CLas are PCR‐based and require purification of DNA from plant samples. Elution of DNA from tissue prints made on nitrocellulose membranes followed by qPCR (TPE‐qPCR) was compared to DNA extraction of plant tissue followed by PCR (X‐PCR) by testing the same tissue samples. The former estimated a higher CLas population in tissue prints than the latter (t‐test; P = 0.009). All extracts prepared for TPE‐qPCR throughout the experiment were also tested by conventional PCR and 80.8% were identified as positive. A similar set of stem and petiole tissue samples was tested by TPE‐qPCR and immunoassay. Although the detection rate by TPE‐qPCR was higher than by immunoassay, about 6% of tissue prints were positive by immunoassay but not by TPE‐qPCR. Thus, a higher detection rate would be achieved by combining TPE‐qPCR with immunoassay. Significant differences were observed in the performance of nitrocellulose membranes from different manufacturers in these assays. Immunotissue prints showed that the spatial distribution pattern of CLas infection varied widely from one sample to another, but the patterns were highly correlated among serial sections from the same sample, suggesting that CLas preferentially colonizes adjacent phloem cells in a vertical rather than horizontal direction.
AbSRiM: An Agent‐Based Security Risk Management Approach for Airport Operations
Authors: Janssen Stef , Sharpanskykh Alexei , Curran Richard 
Published: February 2019

AbstractSecurity risk management is essential for ensuring effective airport operations. This article introduces AbSRiM, a novel agent‐based modeling and simulation approach to perform security risk management for airport operations that uses formal sociotechnical models that include temporal and spatial aspects. The approach contains four main steps: scope selection, agent‐based model definition, risk assessment, and risk mitigation. The approach is based on traditional security risk management methodologies, but uses agent‐based modeling and Monte Carlo simulation at its core. Agent‐based modeling is used to model threat scenarios, and Monte Carlo simulations are then performed with this model to estimate security risks.The use of the AbSRiM approach is demonstrated with an illustrative case study. This case study includes a threat scenario in which an adversary attacks an airport terminal with an improvised explosive device. The approach provides a promising way to include important elements, such as human aspects and spatiotemporal aspects, in the assessment of risk. More research is still needed to better identify the strengths and weaknesses of the AbSRiM approach in different case studies, but results demonstrate the feasibility of the approach and its potential.
Dental management of a child with ectrodactyly ectodermal dysplasia cleft lip/palate syndrome: A case report
Authors: Elhamouly Yasmine , Dowidar Karin ML 
Published: February 2019

AbstractEctrodactyly ectodermal dysplasia with clefting is a rare syndrome resulting from TP63 gene mutations. It is inherited in autosomal dominant manner or as a de novo transfiguration. It is characterized by a triad of ectodermal dysplasia, ectrodactyly, and facial clefts. This report represents a clinical case of 5 years and 6 months‐old male child with ectrodactyly ectodermal dysplasia cleft lip and palate syndrome requiring treatment of his carious teeth. After history taking and clinical examination, the necessary treatment was provided under general anesthesia due to the definitely negative behavior of the child. The treatment outcomes had a positive impact on the behavior and acceptance to dental treatment. This was evidenced by completion of the prosthetic and space management appliances on the dental chair. The child's quality of life was consequently improved. This was evidenced by the reduced response scores of the child perception questionnaire (CPQ11‐14) after treatment. This report highlighted the value of proper diagnosis and fulfillment of the unmet dental needs for patients with orofacial syndromes to improve their quality of life.
The seagrass skeletal assemblage from modern to fossil and from tropical to temperate: Insight from Maldivian and Mediterranean examples
Authors: Brandano Marco , Tomassetti Laura , Mateu‐Vicens Guillem , Gaglianone Giovanni 
Published: February 2019

AbstractSeagrasses are marine angiosperms that form extensive submarine meadows in the photic zone where carbonate producing biota dwell as epiphytes on the leaves or as infaunal forms, and act as prolific carbonate sediment factories. Because seagrasses have a low preservation potential and records of exceptionally well‐preserved and plant material from marine settings are rare, these palaeoenvironments are difficult to identify in the rock record. Consequently, sedimentological and palaeontological proxies are the main indicators of the presence of seagrass‐dominated ecosystems. This work investigates the skeletal assemblage of Modern (Maldivian and western Mediterranean) and fossil (Eocene; Apula and Oman carbonate platforms and Oligocene; Malta platform) seagrass examples to characterize the skeletal assemblage of modern and fossil seagrasses. Two main types of grains, calcareous algae and foraminifera, constitute around 50% of the bioclastic sediment in both tropical Maldivian and temperate Mediterranean scenarios. However, in the tropical setting they are represented by green algae (Halimeda), while in the Mediterranean they are represented by corallinacean red algae. In contrast, in the Eocene examples, the foraminifera are the most conspicuous group and the green algae are also abundant. The opposite occurs in the Maltese Chattian, which is dominated by coralline algae (mean 42%), although the foraminifera are still abundant. It is suggested to use the term foralgal to identify the seagrass skeletal assemblage. To discriminate between red algae and green algae dominance, the introduction of the prefixes ‘GA’ (green algae) and ‘RA’ (red algae) is proposed. The investigated examples provide evidence that the green algae–foralgal assemblage is typical of tropical, not excessively dense seagrass meadows, characterized by a well‐illuminated substrate to support the development and calcification of the Halimeda thallus. Contrarily, the red algae‐foralgal assemblage is typical of high density tropical to subtropical seagrass meadows which create very dense oligophotic conditions on the sea floor or in temperate settings where Halimeda cannot calcify.
A large‐scale circular RNA profiling reveals universal molecular mechanisms responsive to drought stress in maize and Arabidopsis
Authors: Zhang Pei , Fan Yuan , Sun Xiaopeng , Chen Lu , Terzaghi William , Bucher Etienne , Li Lin , Dai Mingqiu 
Published: February 2019

SummaryDrought is a major abiotic stress that threatens global food security. Circular RNAs (circRNAs) are endogenous RNAs. How these molecules influence plant stress responses remains elusive. Here, a large‐scale circRNA profiling identified 2174 and 1354 high‐confidence circRNAs in maize and Arabidopsis, respectively, and most were differentially expressed in response to drought. A substantial number of drought‐associated circRNA‐hosting genes were involved in conserved or species‐specific pathways in drought responses. Comparative analysis revealed that circRNA biogenesis was more complex in maize than in Arabidopsis. In most cases, maize circRNAs were negatively correlated with sRNA accumulation. In 368 maize inbred lines, the circRNA‐hosting genes were enriched for single nucleotide polymorphisms (SNPs) associated with circRNA expression and drought tolerance, implying either important roles of circRNAs in maize drought responses or their potential use as biomarkers for breeding drought‐tolerant maize. Additionally, the expression levels of circRNAs derived from drought‐responsible genes encoding calcium‐dependent protein kinase and cytokinin oxidase/dehydrogenase were significantly associated with drought tolerance of maize seedlings. Specifically, Arabidopsis plants overexpressing circGORK (Guard cell outward‐rectifying K+‐channel) were hypersensitive to abscisic acid, but insensitive to drought, suggesting a positive role of circGORK in drought tolerance. We report the transcriptomic profiling and transgenic studies of circRNAs in plant drought responses, and provide evidence highlighting the universal molecular mechanisms involved in plant drought tolerance.
AtBUD13 affects pre‐mRNA splicing and is essential for embryo development in Arabidopsis
Authors: Xiong Feng , Ren Jing‐Jing , Yu Qin , Wang Yu‐Yi , Kong Lan‐Jing , Otegui Marisa S. , Wang Xiu‐Ling 
Published: February 2019

SummaryPre‐mRNA splicing is an important step for gene expression regulation. Yeast Bud13p (bud‐site selection protein 13) regulates the budding pattern and pre‐mRNA splicing in yeast cells; however, no Bud13p homologs have been identified in plants. Here, we isolated two mutants that carry T‐DNA insertions at the At1g31870 locus and shows early embryo lethality and seed abortion. At1g31870 encodes an Arabidopsis homolog of yeast Bud13p, AtBUD13. Although AtBUD13 homologs are widely distributed in eukaryotic organisms, phylogenetic analysis revealed that their protein domain organization is more complex in multicellular species. AtBUD13 is expressed throughout plant development including embryogenesis and AtBUD13 proteins is localized in the nucleus in Arabidopsis. RNA‐seq analysis revealed that AtBUD13 mutation predominantly results in the intron retention, especially for shorter introns (≤100 bases). Within this group of genes, we identified 52 genes involved in embryogenesis, out of which 22 are involved in nucleic acid metabolism. Our results demonstrate that AtBUD13 plays critical roles in early embryo development by effecting pre‐mRNA splicing.
Computed tomographic dimensions of the normal adult equine eye
Authors: Hollis Anna R. , Dixon Jonathon J. , Berlato Davide , Murray Rachel , Weller Renate 
Published: February 2019

AbstractThere are limited data on whether the dimensions of the equine eye and its internal structures change with bodyweight in horses. The aim of this study was to identify whether the size of the equine eye and its individual structures varied in a predictable manner with bodyweight, and to examine the reliability of computed tomography (CT) scans in the measurement of the equine eye. Ninety horses which had undergone CT examination of the head for non‐ocular disease were included. All measurements of the eye were performed twice on all eyes by the same operator to quantify intra‐operator agreement, and in 10 cases were also performed by a second operator to quantify inter‐operator agreement. Agreement was excellent for all but the rostrocaudal measurement of the anterior chamber, which was fair. The following variables correlated significantly with bodyweight: anterior‐posterior size of the globe (correlation coefficient: 0.586) and posterior segment (correlation coefficient: 0.554); the latero‐medial size of the globe (correlation coefficient: 0.452), anterior chamber (correlation coefficient: 0.504) and posterior segment (correlation coefficient: 0.455); and the orbital fossa diameter (correlation coefficient: 0.219). The lens size and anterior‐posterior distance of the anterior chamber did not correlate significantly with bodyweight. These results suggest that overall eye size and the size of the orbital fossa change with the bodyweight of the horse, but lens size remains consistent, and that CT measurements of the internal structures of the eye are repeatable and reproducible. This information aids in interventional procedures for ocular pathology and assessment of normal anatomy.
Subconjunctival bone marrow‐derived mesenchymal stem cell therapy as a novel treatment alternative for equine immune‐mediated keratitis: A case series
Authors: Davis Amanda B. , Schnabel Lauren V. , Gilger Brian C. 
Published: February 2019

AbstractEquine immune‐mediated keratitis (IMMK) leads to increased corneal opacity and inflammation secondary to an alteration of the local immune system. Bone marrow‐derived mesenchymal stem cells (BM‐MSC) have been shown to modulate the immune system by downregulating inflammation. Four horses with unilateral IMMK poorly responsive to traditional medical treatments underwent novel, autologous subconjunctival BM‐MSC therapy. Bone marrow was harvested and processed as previously described for equine orthopedic disease. Horses received autologous subconjunctival BM‐MSC injections approximately every 3‐4 weeks for 1‐5 treatments total. Horses were maintained on their current medical treatment regimen throughout the BM‐MSC treatment period. Three horses had a positive response to therapy as demonstrated by an increase in corneal clarity, a decrease in neovascularization and a reduction in surface irregularity. One horse was nonresponsive to therapy. These experimental results demonstrate the safety and potential efficacy of an innovative solution for IMMK.
Use of 1% polidocanol and pre‐ and post‐computed tomography for treatment of a suspected nasolacrimal duct cyst in a dog
Authors: Zimmerman Kelli L. , Stefanacci Joseph D. , Greenberg Shari M. 
Published: February 2019

AbstractObjectiveTo describe the efficacy of the sclerosing agent 1% polidocanol in the treatment of a suspected nasolacrimal duct cyst in a dog.Animal StudiedA 5‐year‐old castrated male Golden Retriever with chronic epiphora of the right eye.ProceduresOcular examination revealed epiphora and a negative Jones test of the right eye and was otherwise normal. Computed tomography with dacryocystography confirmed a cystic structure in the right ventral orbit that extended into the caudal nasal cavity adjacent to the orbit, causing partial physical obstruction of the right nasolacrimal duct. Cytologic analysis of fluid from the lesion was supportive of a diagnosis of a cyst. One percent polidocanol (compounded, People's Custom Rx, Memphis, TN) was injected into the cyst.ResultsEpiphora was resolved by two weeks post‐injection. Repeated computed tomography with dacryocystography was performed 8 months post‐injection, revealing complete resolution of the cyst and demonstrating mild enophthalmos of the right globe.ConclusionsIntralesional 1% polidocanol therapy was successful in resolving a suspected nasolacrimal duct cyst in a dog.
Ocular dermoids in dogs: A retrospective study
Authors: Badanes Zachary , Ledbetter Eric C. 
Published: February 2019

AbstractObjectiveTo describe clinical features of dogs diagnosed with ocular dermoids at two veterinary teaching hospitals.Animals studiedRetrospective case series of 44 dogs (49 dermoids) with ocular dermoids.ProceduresMedical records of dogs evaluated by the Cornell University and University of Pennsylvania ophthalmology services were evaluated to identify dogs with a clinical diagnosis of ocular dermoids between 2004 and 2018, and 2011 and 2018, respectively. Signalment, historical, and clinical details were recorded, including dermoid location, concurrent diseases, treatment, histopathologic findings, and outcome.ResultsA total of 49 ocular dermoids, involving 47 eyes, were diagnosed in 44 dogs. The mean ( standard deviation) age of the study population at the time of diagnosis was 1.19 years (1.85 years). Of the 44 dogs evaluated, 28 (63.6%) were male and 30 (68.2%) were intact at time of diagnosis. Twenty‐two different breeds were represented in the study, with mixed breed, French Bulldog, and Shih Tzu being the most common. Twenty‐two dermoids were categorized as limbal (44.9%), 14 as eyelid (28.6%), eight as corneal (16.3%), and five as conjunctival (10.2%). Concurrent ocular findings were noted in 29 of the 47 eyes (61.7%), including corneal pigmentation, epiphora, and conjunctival hyperemia. Nine dogs (20.5%) suffered from concurrent systemic disease, with the majority being cardiac in origin. A total of 34 dermoids (69.4%) were surgically excised with no recurrences.ConclusionsOcular dermoids are an uncommon condition in dogs. Concurrent congenital cardiac disease was relatively common in the dogs of this study. Surgical excision of dermoids was curative.