bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Borrelia burgdorferi mini‐vls system that undergoes antigenic switching in mice: investigation of the role of plasmid topology and the long inverted repeat
Authors: Castellanos Mildred , Verhey Theodore B. , Chaconas George 
Published: July 2018

SummaryBorrelia burgdorferi evades the host immune system by switching the surface antigen. VlsE, in a process known as antigenic variation. The DNA mechanisms and genetic elements present on the vls locus that participate in the switching process remain to be elucidated. Manipulating the vls locus has been difficult due to its instability on Escherichia coli plasmids. In this study, we generated for the first time a mini‐vls system composed of a single silent vlsE variable region (silent cassette 2) through the vlsE gene by performing some cloning steps directly in a highly transformable B. burgdorferi strain. Variants of the mini system were constructed with or without the long inverted repeat (IR) located upstream of vlsE and on both circular and linear plasmids to investigate the importance of the IR and plasmid topology on recombinational switching at vlsE. Amplicon sequencing using PacBio long read technology and analysis of the data with our recently reported pipeline and VAST software showed that the system undergoes switching in mice in both linear and circular versions and that the presence of the hairpin does not seem to be crucial in the linear version, however it is required when the topology is circular.
Nuclear export‐dependent degradation of the carbon catabolite repressor CreA is regulated by a region located near the C‐terminus in Aspergillus oryzae
Authors: Tanaka Mizuki , Ichinose Sakurako , Shintani Takahiro , Gomi Katsuya 
Published: July 2018

SummaryCarbon catabolite repression (CCR) is regulated by the C2H2‐type transcription factor CreA/Cre1 in filamentous fungi including Aspergillus oryzae. We investigated the stability and subcellular localization of CreA in A. oryzae. The abundance of FLAG‐tagged CreA (FLAG‐CreA) was dramatically reduced after incubation in maltose and xylose, which stimulated the export of CreA from the nucleus to the cytoplasm. Mutation of a putative nuclear export signal resulted in nuclear retention and significant stabilization of CreA. These results suggest that CreA is rapidly degraded in the cytoplasm after export from the nucleus. The FLAG‐CreA protein level was reduced by disruption of creB and creC, which encode the deubiquitinating enzyme complex involved in CCR. In contrast, FLAG‐CreA stability was not affected by disruption of creD which encodes an arrestin‐like protein required for CCR relief. Deletion of the last 40 C‐terminal amino acids resulted in remarkable stabilization and increased abundance of FLAG‐CreA, whereas deletion of the last 20 C‐terminal amino acids had no apparent effect on CreA stability. This result suggests that the 20 amino acid region located between positions 390 and 409 of CreA is critical for the rapid degradation of CreA.
Fungal keratitis: An overview of clinical and laboratory aspects
Authors: Mahmoudi Shahram , Masoomi Ahmad , Ahmadikia Kazem , Tabatabaei Seyed Ali , Soleimani Mohammad , Rezaie Sassan , Ghahvechian Hossein , Banafsheafshan Ali 
Published: July 2018

SummaryMycotic keratitis or keratomycosis is a fungal infection with global distribution. The dominant aetiology of this disease varies based on geographical origin, socioeconomic status, and climatic condition. Generally, Aspergillus spp. and Fusarium spp. are common in tropical and subtropical regions and Candida spp. are dominant in temperate areas. Demonstration of fungal elements in microscopic examination besides the isolation of fungi in culture is the gold standard of laboratory diagnosis. As the culture is a time‐consuming procedure, other approaches such as in vivo confocal microscopy which produces real‐time imaging of corneal tissue and molecular techniques have been developed to facilitate rapid diagnosis of fungal keratitis. The first choice of treatment is topical natamycin, although topical amphotericin B is the best choice for Aspergillus and Candida keratitis. Regarding the diversity of fungal aetiology and the emergence of drug resistance in some genera and species, proper identification using molecular methods and antifungal susceptibility testing could provide useful data. Furthermore, as the better efficacy of combination therapy in comparison to monotherapy is reported, in vitro determination of interactions between various drugs seem informative. This review aims to provide a general and updated view on the aetiology, risk factors, epidemiology, clinical and laboratory diagnosis, and management of fungal keratitis.
Narrow‐band imaging pattern classification in oral cavity
Authors: Tirelli Giancarlo , Marcuzzo Alberto Vito , Boscolo Nata Francesca 
Published: July 2018

AbstractObjectiveNarrow‐band imaging is widely used in the diagnostic work‐up of oral lesions. Different oral subsites present three epithelial types (1, 2a and 2b), each with a different structure and function. The aim of this study was to analyse and describe the different vascular patterns seen on narrow‐band imaging according to oral epithelial type and histology.Materials and MethodsThe narrow‐band imaging photographs of healthy, dysplastic and neoplastic oral mucosa were retrospectively reviewed and divided according to epithelial type and histology. The different narrow‐band imaging patterns were analysed, related to the clinical appearance of the specific area, accurately described and drawn by a professional designer.ResultsThe photographs of 302 patients were considered. Six patterns were identified: Normal mucosa exhibited different appearance in each type of epithelium; dysplastic mucosa presented the same pattern in type 1 and 2a epithelia, which differed from that of type 2b epithelium; in cancer, mucosal appearance was identical irrespective of epithelial type, due to complete vascular destruction.ConclusionsThe proposed classification could serve as a guide for clinicians approaching narrowband imaging, especially at early stages of the learning curve, to differentiate normal mucosa from malignant lesions and possibly reduce the number of unnecessary biopsies.
Pharmacogenetics of inhaled long‐acting beta2‐agonists in asthma: A systematic review
Authors: Slob Elise M. A. , Vijverberg Susanne J. H. , Palmer Colin N. A. , Zazuli Zulfan , Farzan Niloufar , Oliveri Nadia M. B. , Pijnenburg Mariëlle W. , Koppelman Gerard H. , Maitland‐van der Zee Anke H. 
Published: July 2018

AbstractBackgroundLong‐acting beta2‐agonists (LABA) are recommended in asthma therapy; however, not all asthma patients respond well to LABA. We performed a systematic review on genetic variants associated with LABA response in patients with asthma.MethodsArticles published until April 2017 were searched by two authors using PubMed and EMBASE. Pharmacogenetic studies in patients with asthma and LABA response as an outcome were included.ResultsIn total, 33 studies were included in this systematic review; eight focused on children (n = 6051). Nineteen studies were clinical trials, while 14 were observational studies. Studies used different outcomes to define LABA response, for example, lung function measurements (FEV1, PEF, MMEF, FVC), exacerbations, quality of life, and asthma symptoms. Most studies (n = 30) focused on the ADRB2 gene, encoding the beta2‐adrenergic receptor. Thirty studies (n = 14 874) addressed ADRB2 rs1042713, 7 ADRB2 rs1042714 (n = 1629), and 3 ADRB2 rs1800888 (n = 1892). The association of ADRB2 rs1042713 and rs1800888 with LABA response heterogeneity was successfully replicated. Other variants were only studied in three studies but not replicated. One study focused on the ADCY9 gene. Five studies and a meta‐analysis found an increased risk of exacerbations in pediatrics using LABA carrying one or two A alleles (OR 1.52 [1.17; 1.99]). These results were not confirmed in adults.ConclusionsADRB2 rs1042713 variant is most consistently associated with response to LABA in children but not adults. To assess the clinical value of ADRB2 rs1042713 in children with asthma using LABA, a randomized clinical trial with well‐defined outcomes is needed.
Interspecific compatibility barriers, development of interspecific hybrids through embryo rescue and lineage ofTrifolium alexandrinum(Egyptian clover)—important tropical forage legume
Authors: Malaviya Devendra R. , Roy Ajoy K. , Kaushal Pankaj , Chakraborti Mridul , Yadav Aradhana , Khare Ambica , Dhir Richa , Khairnar Dushyant , George Ginu Percis 
Published: July 2018

AbstractGenetic improvement ofTrifolium alexandrinumL. is hampered because of narrow genetic base and lack of interspecies compatibility information. The study was envisaged to understand the interspecies incompatibility and the affinity betweenT. alexandrinumand 22 species of the genus representing different sections and to develop interspecific crosses. Development of interspecific hybrids withT. resupinatum, T. lappaceum, T. subterraneum, T. vesiculosumandT. echinatum,through embryo rescue, revealed their affinity withT. alexandrinum. Failure of pollen germination or restricted pollen tube growth showed its distant relatedness withT. clypeatum, T. balansae, T. purpureum, T. leucanthum, T. hirtum, T. pilulareandT. hybridum. Pollen tubes reached up to ovule among the crosses withT. alpestre, T. repensandT. nigrescens,whereas it travelled up to ovary among the crosses withT. angustifolium, T. grandiflorumandT. dasyurumindicating need of manipulation to overcome barrier. Thus, incompatibility ofT. alexandrinumwith manyTrifoliumspecies could be overcome through embryo rescue with intensive crossing. Egyptian clover ecotype ‘Fahli’ was more compatible with other species than ‘Mescavi’.
Characterization of broad‐spectrum resistance to Soybean mosaic virus in soybean [Glycine max (L.) Merr.] cultivar ‘RN‐9’
Authors: Ren Rui , Yin Jinlong , Zheng Huanfang , Wang Tao , Liu Shichao , Karthikeyan Adhimoolam , Yang Qinghua , Gao Le , Zhi Haijian , Li Kai 
Published: July 2018

AbstractSoybean mosaic virus (SMV) can cause serious yield losses in soybean. Soybean cultivar ‘RN‐9’ is resistant to 15 of 21 SMV strains. To well‐characterize this invaluable broad‐spectrum SMV‐resistance, populations (F1, F2 and F2:3) derived from resistant (R) × susceptible (S) and R × R crosses were tested for SMV‐SC18 resistance. Genetic analysis revealed that SC18 resistance in ‘RN‐9’ plus two elite SMV‐resistant genotypes (‘Qihuang No.1’ and ‘Kefeng No.1’) are controlled by independently single dominant genes. Linkage analysis showed that the resistance of ‘RN‐9’ to SMV strains SC10, SC14, SC15 and SC18 is controlled by more than one gene(s). Moreover, Rsc10‐r and Rsc18‐r were both positioned between the two simple sequence repeats markers Satt286 and Satt277, while Rsc14‐r was fine‐mapped in 136.8‐kb genomic region containing sixteen genes, flanked by BARCSOYSSR_06_0786 and BARCSOYSSR_06_0790 at genetic distances of 3.79 and 4.14 cM, respectively. Allelic sequence comparison showed that Cytochrome P450‐encoding genes (Glyma.06g176000 and Glyma.06g176100) likely confer the resistance to SC14 in ‘RN‐9’. Our results would facilitate the breeding of broad‐spectrum and durable SMV resistance in soybeans.
Carbon and oxygen isotope fractionations in tree rings reveal interactions between cambial phenology and seasonal climate
Authors: Belmecheri Soumaya , Wright William E. , Szejner Paul , Morino Kiyomi A. , Monson Russell K. 
Published: July 2018

AbstractWe developed novel approaches for using the isotope composition of tree‐ring subdivisions to study seasonal dynamics in tree–climate relations. Across a 30‐year time series, the δ13C and δ18O values of the earlywood (EW) cellulose in the annual rings of Pinus ponderosa reflected relatively high intrinsic water‐use efficiencies and high evaporative fractionation of 18O/16O, respectively, compared with the false latewood (FLW), summerwood (SW), and latewood (LW) subdivisions. This result is counterintuitive, given the spring origins of the EW source water and midsummer origins of the FLW, SW, and LW. With the use of the Craig–Gordon (CG), isotope‐climate model revealed that the isotope ratios in all of the ring subdivision are explained by the existence of seasonal lags, lasting several weeks, between the initial formation of tracheids and the production of cellulosic secondary cell walls during maturation. In contrast to some past studies, modification of the CG model according to conventional methods to account for mixing of needle water between fractionated and nonfractionated sources did not improve the accuracy of predictions. Our results reveal new potential in the use of tree‐ring isotopes to reconstruct past intra‐annual tree–climate relations if lags in cambial phenology are reconciled with isotope ratio observations and included in theoretical treatments.
Outcome of treosulfan‐based reduced‐toxicity conditioning regimens for HSCT in high‐risk patients with primary immune deficiencies
Authors: Haskoloğlu Şule , Köstel Bal Sevgi , İslamoğlu Candan , Altun Demet , Kendirli Tanıl , Doğu Esin Figen , İkincioğulları Aydan 
Published: July 2018

AbstractIntroductionHSCT is the curative therapeutic option in PIDs. Due to the increase in survival rates, reduced‐toxicity conditioning regimens with treosulfan have become another alternative. The purpose of this retrospective study was to analyze the outcome of treosulfan‐based conditioning before HSCT for patients with PID.MethodA total of 15 patients that received a treosulfan‐based conditioning regimen for HSCT were recruited. Type of diagnosis, donor and stem cell source, pretransplant organ damage, infections, engraftment, chimerism, and transplant‐related toxicities were analyzed.ResultsAt a median follow‐up time of 32 months, the overall survival was 86.7%. Following HSCT, 14 of 15 patients had engraftment, with 86.7% of the cohort having full‐donor chimerism. The most common toxicity was seen on the skin (53.3%). Acute GVHD and chronic GVHD were documented in 53% and 20% of the study population, respectively. Although the cohort consisted of patients with pretransplant liver damage, SOS manifestations were documented in 20%.ConclusionTreosulfan‐based conditioning regimens before HSCT are associated with lower toxicity compared to myeloablative regimens, are safe, and have high engraftment rates with full‐donor chimerism in patients having PID, regardless of the specified genetic diagnosis and donor type.
Transcatheter stenting of superior vena cava obstruction after pediatric heart transplantation: A single‐center experience assessing risk factors and outcomes
Authors: Salavitabar Arash , Flyer Jonathan N. , Torres Alejandro J. , Richmond Marc E. , Crystal Matthew A. , Turner Mariel E. , Chai Paul , Zuckerman Warren A. 
Published: July 2018

AbstractTranscatheter stent implantation for SVC obstruction following OHT has been well described, particularly in pediatric patients. This study describes a large single‐center pediatric heart transplant experience that investigates the risk factors for SVC stenosis requiring stent implantation and its associated outcomes. All pediatric OHTs between January 1, 2000, and December 12, 2016, were examined for risk factors. Twelve of 349 (3.4%) OHTs required SVC stent implantation. Patients who required stents were younger (2.5 years vs 10.0 years, P = 0.0097), weighed less (8.6 kg vs 26.0 kg, P = 0.0024), and were more likely to have had CHD (83% vs 32%, P = 0.001) or previous SCPA (58% vs 18%, P = 0.002). Bicaval anastomosis was not associated with subsequent SVC stent implantation. Symptoms included SVC syndrome and chylous effusions. All 12 patients had evidence of significant SVC obstruction by both echocardiographic Doppler interrogation and transcatheter angiography. There were no acute procedural complications; however, reinterventions were common (four of 12 patients) and occurred at a mean of 5.7 ± 3.6 months poststent implantation. In conclusion, transcatheter SVC stent implantation is safe and effective after OHT. There were significant associations between SVC stent implantation and younger age, smaller weight, CHD, and history of SCPA, but not with bicaval anastomosis or donor‐recipient weight ratio.
Hypoxia and the group VII ethylene response transcription factor HRE2 promote adventitious root elongation inArabidopsis
Authors: Eysholdt‐Derzsó E. , Sauter M. 
Published: July 2018

AbstractSoil water‐logging and flooding are common environmental stress conditions that can impair plant fitness. Roots are the first organs to be confronted with reduced oxygen tension as a result of flooding. While anatomical and morphological adaptations of roots are extensively studied, the root system architecture is only now becoming a focus of flooding research. Adventitious root (AR) formation shifts the root system higher up the plant, thereby facilitating supply with oxygen, and thus improving root and plant survival.We usedArabidopsisknockout mutants and overexpressors of ERFVII transcription factors to study their role in AR formation under hypoxic conditions and in response to ethylene.Results show that ethylene inhibits AR formation. Hypoxia mainly promotes AR elongation rather than formation mediated by ERFVII transcription factors, as indicated by reduced AR elongation inerfVIIseedlings. Overexpression of HRE2 induces AR elongation to the same degree as hypoxia, while ethylene overrides HRE2‐induced AR elongation.The ERFVII transcription factors promote establishment of an AR system that is under negative control by ethylene. Inhibition of growth of the main root system and promotion of AR elongation under hypoxia strengthens the root system in upper soil layers where oxygen shortage may last for shorter time periods.
Disease state changes and safety of long‐term donepezil hydrochloride administration in patients with Alzheimer's disease: Japan‐Great Outcome of Long‐term trial with Donepezil (J‐GOLD)
Authors: Arai Heii , Hashimoto Naoyuki , Sumitomo Kenta , Takase Takao , Ishii Mika 
Published: July 2018

BackgroundA long‐term, large‐scale study of donepezil hydrochloride in patients with Alzheimer's disease (AD) was conducted. Previously, two interim reports were published during this study. We have now completed the study and herein present our analysis of the final results.MethodsThe subjects of this study included AD patients who received the drug for the first time (newly treated patients), as well as AD patients who were already receiving the drug at the start of the study (continuously treated patients). The observation period was 48 months. Changes in cognitive function and severity of dementia associated with the drug administration and its safety were assessed.ResultsCognitive function decreased significantly after 24 months in newly treated patients and after 6 months in continuously treated patients, compared with baseline. The percentages of patients whose dementia severity improved or remained the same compared with baseline were 59.27% at 48 months in the newly treated patients and 57.09% at 48 months in the continuously treated patients. There were no major safety problems with the drug.ConclusionsWe conducted a large‐scale study of AD patients in Japan. Here, we present our analysis of the final results and describe current clinical practice with the drug, changes in cognitive function and dementia severity associated with long‐term administration of the drug, and the drug's safety.
The monocyte locomotion inhibitory factor inhibits the expression of inflammation‐induced cytokines following experimental contusion in rat tibia
Authors: Rojas‐Dotor Sara , Araujo‐Monsalvo Víctor Manuel , Sánchez‐Rojas Marco Julio , Domínguez‐Hernández Víctor Manuel 
Published: July 2018

AbstractEntamoeba histolityca produces the monocyte locomotion inhibitory factor (MLIF), a pentapeptide with powerful anti‐inflammatory properties. MLIF may regulate trauma‐induced inflammation through the effects it exerts directly or indirectly on immune cells, modulating the production and/or expression of the cytokines involved in the inflammatory processes that occur after damage. The aim of the present study was to evaluate the effect of MLIF on production of pro/anti‐inflammatory cytokines after contusion in the rat tibia. Fifty‐four Wistar rats were subjected to controlled contusion with a special guillotine‐type device, and 36 rats were injected with MLIF or tenoxicam into the tibia. Eighteen animals received saline; the animals were sacrificed 24 or 48 hours after injection. Cytokine mRNA and protein production were determined by reverse transcriptase‐polymerase chain reaction (RT‐PCR), immunofluorescence, and hematoxylin‐eosin staining was performed to visualize cellular infiltration in the rats’ injured tissue. Expression levels of the cytokines interferon gamma (IFN‐γ), tumour necrosis factor‐alpha (TNF‐α), interleukin‐6 (IL‐6) and transforming growth factor‐beta (TGF‐β) mRNA were inhibited significantly by MLIF at 24 hours post‐contusion. MLIF significantly increased the expression levels of IL‐10 at 24 hours compared with tenoxicam or the control group. These changes were associated with a significant decrease in protein production levels of TNF‐α, IFN‐γ, IL‐6 and TGF‐β at 24 hours. Histological evaluation showed the presence of infiltration by neutrophils, monocytes and leucocytes in control tissues. This infiltration was decreased after MLIF administration, and intense infiltration was observed in tenoxicam‐treated group. MLIF inhibited the expression of pro‐inflammatory cytokines and increased the expression of anti‐inflammatory cytokine IL‐10.
The performance of the Australian welfare system in a time of neoliberal economic reform
Authors: Tapper Alan 
Published: July 2018

Abstract“Neoliberalism”, both as a body of theory and as a set of policies and practices, is commonly seen as unsympathetic, even antagonistic, to the welfare state. In the period from the mid‐1980s to the global financial crisis of 2007–08, Australia underwent very considerable “neoliberal” economic policy reform. What happened to the Australian welfare system and to Australia's socioeconomic egalitarianism in this period? To shed light on that question three kinds of trend are tracked. The first is household taxes and social expenditure in both cash and kind, using fiscal incidence analysis where the main metric is “net benefits”. The second is economic inequality, as measured by the distribution of incomes and wealth. The third is the performance of the labor market, as measured by earned incomes and unemployment rates. The article concludes with an attempt to integrate the evidence collected from these three sources. The general conclusion is that the Australian welfare system did not follow the pessimists' predictions. The welfare system grew in size and redistributive quantum. Wage levels rose strongly, while unemployment rates fell. Overall, income inequality increased to a small extent, though mainly before the full economic reform process was in place, while wealth inequality changed little.