bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation
Authors: Delmore Kira E. , Hübner Sariel , Kane Nolan C. , Schuster Richard , Andrew Rose L. , Câmara Francisco , Guigó Roderic , Irwin Darren E. 
Published: March 2015

AbstractDifferential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole‐genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.
Rapid diversification associated with ecological specialization in NeotropicalAdelphabutterflies
Authors: Ebel Emily R. , DaCosta Jeffrey M. , Sorenson Michael D. , Hill Ryan I. , Briscoe Adriana D. , Willmott Keith R. , Mullen Sean P. 
Published: March 2015

AbstractRapid diversification is often associated with morphological or ecological adaptations that allow organisms to radiate into novel niches. NeotropicalAdelphabutterflies, which comprise over 200 species and subspecies, are characterized by extraordinary breadth in host plant use and wing colour patterns compared to their closest relatives. To examine the relationship between phenotypic and species diversification, we reconstructed the phylogenetic history ofAdelphaand its temperate sister genusLimenitisusing genomewide restriction‐site‐associatedDNA(RAD) sequencing. Despite a declining fraction of shared markers with increasing evolutionary distance, theRAD‐Seq data consistently generated well‐supported trees using a variety of phylogenetic methods. These well‐resolved phylogenies allow the identification of an ecologically important relationship with a toxic host plant family, as well as the confirmation of widespread, convergent wing pattern mimicry throughout the genus. Taken together, our results support the hypothesis that evolutionary innovations in both larvae and adults have permitted the colonization of novel host plants and fuelled adaptive diversification within this large butterfly radiation.
Hexokinase plays a critical role in deoxynivalenol (DON) production and fungal development in Fusarium graminearum
Authors: Zhang Leigang , Li Baicun , Zhang Yu , Jia Xiaojing , Zhou Mingguo 
Published: March 2015

SummaryFusarium graminearum, the causal agent of Fusarium head blight, is a common pathogen on small grain cereals worldwide and produces various trichothecenes [deoxynivalenol (DON) is predominant] during infection. A previous study has revealed that DON production is positively correlated with the occurrence of carbendazim (MBC) resistance. Here, we identified and characterized two putative genes encoding hexokinase in F. graminearum (FgHXK1 and FgHXK2), which is a rate‐limiting enzyme in DON biosynthesis. The expression level of hexokinase genes and the production of pyruvate, which is the precursor of DON, were up‐regulated in the MBC‐resistant strain, indicating that hexokinase genes might be involved in increased DON production. Phylogenetic and comparative analyses indicated that FgHXK1 was the predominant hexokinase gene. Gene disruption showed that ΔFgHXK1 severely affected DON production, indicating that FgHXK1 played a role in the regulation of DON biosynthesis. Morphological characterization showed that ΔFgHXK1 led to inhibited vegetative growth and conidiation. Sensitivity tests to MBC and various stresses indicated that both ΔFgHXK1 and ΔFgHXK2 mutants showed no significant difference from parental strains. Pathogencity assays showed that ΔFgHXK1 mutants lost virulence on wheat head and corn stigma; however, they showed no change in sexual reproduction. The FgHXK1‐overexpressing transformants were obtained subsequently. Their pyruvate and DON production was confirmed to be increased, indicating that FgHXK1 positively regulated DON biosynthesis. Although additional defects appeared in overexpression mutants, MBC sensitivity showed no change. All of the results indicated that the transcriptional level of FgHXK1 regulated DON biosynthesis, but showed no direct relationship with MBC resistance.
Molecular characterisation of clinical Cryptococcus neoformans and Cryptococcus gattii isolates from Sichuan province, China
Authors: Wu Si‐Ying , Lei Yao , Kang Mei , Xiao Yu‐Ling , Chen Zhi‐Xing 
Published: March 2015

SummaryPrevious reports on the molecular characteristics of clinical isolates of Cryptococcus species in China have focused on isolates from southeast China. To obtain a more detailed molecular epidemiology, a total of 92 cryptococcal isolates were collected from Sichuan province. A total of 24 isolates from 12 other provinces were collected for comparative study. Genotypes and mating types of 116 Cryptococcus isolates were determined. Among the 116 isolates, 43 isolates (19 isolates from Sichuan and 24 isolates outside of Sichuan) were analysed by multi‐locus sequence typing (MLST). All 116 clinical isolates were mating type α. Most isolates (114/116) were molecular type VNI and the remaining two isolates were VGI and VGII respectively. MLST results revealed five sequence types (STs) of C. neoformans including two novel STs, with most isolates identified as ST5. The two C. gattii isolates identified in our study were ST44 and ST159. Based on our report and previous studies, there are 15 C. neoformans STs in China which can be divided into three subgroups. The C. gattii isolate from Sichuan could be a scattered subtype of VGII (ST44). Our findings demonstrated that C. neoformans isolates in Sichuan are genetically homogeneous, and ST5 is the epidemic clone of C. neoformans in China.
Our 2015 approach to invasive pulmonary aspergillosis
Authors: Liss B. , Vehreschild J. J. , Bangard C. , Maintz D. , Frank K. , Grönke S. , Michels G. , Hamprecht A. , Wisplinghoff H. , Markiefka B. , Hekmat K. , Vehreschild M. J. G. T. , Cornely O. A. 
Published: March 2015

SummaryAt the University Hospital of Cologne, in general two patient groups at high risk for invasive aspergillosis receive posaconazole prophylaxis: Acute myelogenous leukaemia patients during remission induction chemotherapy and allogeneic haematopoietic stem cell transplant recipients. Other patients at risk undergo serum galactomannan testing three times weekly. At 72–96 h of persisting fever despite broad‐spectrum antibiotics, or at onset of lower respiratory tract symptoms a thoracic computed tomography (CT) scan is performed. Without lung infiltrates on CT, IPA is ruled out. In lung infiltrates not suggestive for IPA mycological confirmation is pursued. In patients without posaconazole prophylaxis empiric caspofungin will be considered. CT findings typical for IPA prompt targeted treatment, and mycological confirmation. Bronchoalveolar lavage (BAL) is most important for cultural identification and susceptibility testing, and facilitates diagnosing other pathogens. BAL performance is virtually independent of platelet counts. If despite suggestive infiltrates BAL does not yield the diagnosis, CT‐guided biopsy follows as soon as platelet counts allow. Surgery can also be beneficial in diagnosis and treatment of IPA. If the diagnosis of IPA is not established, mucormycosis is a valid concern. In patients with breakthrough IPA during posaconazole prophylaxis liposomal amphotericin B is the drug of choice. If no posaconazole prophylaxis was given, voriconazole is the treatment of choice for IPA.
Hospital environment fungal contamination and aspergillosis risk in acute leukaemia patients in Sousse (Tunisia)
Authors: Gheith Soukeina , Ranque Stéphane , Bannour Wadiaa , Ben Youssef Yosra , Khelif Abderrahim , Ben Said Moncef , Njah Mansour , Saghrouni Fatma 
Published: March 2015

SummaryHospital environment is considered the main source of invasive aspergillosis (IA) in leukemic patients. This study aimed to describe Aspergillus colonisation in leukemic patients and their hospital environment and to test whether Aspergillus environmental contamination was associated with IA. For a 2‐year period including 14‐month renovation work, 91 acute leukaemia inpatients at the hematology department of University hospital in Sousse (Tunisia) were prospectively included. The incidence of probable IA (EORTC/MSG criteria) was 9.9%. Fifty‐six Aspergillus were isolated from 53 (6.5%) of 811 sputa collected from 35 (38.5%) patients. Aspergillus spp. were isolated in 59.7% of 494 air samples and in 52.8% of 1579 surface samples taken in the patients' room. Aspergillus section Nigri (72.7%) was the most frequent. Aspergillus contamination peaked in autumn and winter on surface and in summer and autumn in air samples and was higher (P = 0.03) during the renovation work period. Multivariate analysis showed that for each Aspergillus section Nigri CFU airborne contamination IA risk increased by 1.05 (P = 0.04). In Tunisia, Aspergillus section Nigri and Flavi, but not Fumigati, are chiefly involved in IA. Our findings support swift implementation of airborne fungal contamination control measures in areas where immunocompromised patient are hospitalised.
Millennium development goals (MDGs) and indigenous peoples' literacy in Cambodia: erosion of sovereignty?
Authors: Christie Ryerson 
Published: March 2015

AbstractNation‐building throughout Southeast Asia has been undertaken in contexts where minority groups, living on the margins of society, are being forced into recent state constructions, and have had their cultures eroded as a result. The Millennium Development Goals (MDGs) for education have provided international benchmarks for literacy. These have been adopted by the Cambodian state, and a number of donors and NGOs have funded and enacted policies with the explicit aim of improving the language skills of Cambodia's highland communities. However, these are being implemented in communities that do not speak Khmer (the Cambodian national language), and do not have indigenous systems of writing. Drawing on fieldwork in Cambodia, this paper argues that the impact of the MDGs has been to depoliticize an inherently contested terrain, and to ironically silence communities on fundamental issues by teaching them to read, write and speak the national language. This has limited their capacity to perform sovereignty by restricting the very voice they are entitled to speak.
Borders and banknotes: the national perspective
Authors: First Anat , Sheffi Na'ama 
Published: March 2015

AbstractReplacing a banknotes series is meaningful for politicians and the general public even today, while most transactions are executed through virtual means. The choice of images carried on banknotes represents the limits of the State's sovereign border and becomes a means of banal nationalism. Moreover, by utilising scopic regimes, the hegemony portrays the cultural and political borders: historical figures from the country's past on one side, and an imagined or physical border, expressed through the illustrations on the back. This paper addresses the latter and examines the case of the State of Israel. The analysis of sites and landscapes that appear on national banknotes can decipher the construction process of a ‘territorial identity’ which, along with struggles for maintaining identity, provides the basis of the nation‐state. Using Williams's typology of selective tradition, we argue that Israeli banknotes demonstrate a mixture of residual and new cultural content.
‘Oh motherland I pledge to thee …’: a study into nationalism, gender and the representation of an imagined family within national anthems
Authors: Lauenstein Oliver , Murer Jeffrey S. , Boos Margarete , Reicher Stephen 
Published: March 2015

AbstractIn this paper, we argue that beyond understanding nations as imagined communities, the metaphor of an ‘imagined family’ or ‘filial community’ is a more useful concept towards understanding links between gender and nationhood as family relations in four ways: (1) providing a clear, hierarchical structure; (2) prescribing social roles and responsibilities; (3) being linked to positive affective connotations; and (4) reifying social phenomena as biologically determined. In order to empirically substantiate our claim, we will explore the prevalence and use of family metaphors in a key symbol of nationhood discourses. Through a qualitative analysis of national anthems as ‘mnemonics of national identity’, we demonstrate the widespread presence of family metaphors, discussing how they reproduce ideas of family and gender. Finally, we discuss how the ‘imagined family’ as present in anthems and other forms of national representation could inform future studies of nationalism and national politics.
Managing psychosis in a renal transplant recipient with bipolar affective disorder and allograft rejection
Authors: Dave Vatsa , Mulley William , Kanellis John , Summers Shaun 
Published: March 2015

AbstractManagement of mental health issues in the post‐transplant setting can be difficult given the potential for medication related neurotoxicity. The lack of established guidelines in this area further compounds this difficulty. The current report details the course of patient with stable bipolar affective disorder prior to renal transplantation, who developed de novo psychosis post‐transplantation as an adverse effect of her tacrolimus therapy. The patient was unable to take her usual oral immunosuppressants due to the severity of her psychosis and she eventually required alemtuzumab parenterally as rescue therapy from rejection. This case highlights the diagnostic and therapeutic challenges when dealing with transplant recipients with significant psychosis.
Renal allograft re‐use and herpetic re‐infection
Authors: Setyapranata Stella , Holt Stephen G , Wiggins Kate J , Mulley William R , Kerr Peter G , Landgren Anthony J , Eisen Damon P , Young Andrew , Opdam Helen , Robertson Amanda , Asadi Khashayar , Hughes Peter D 
Published: March 2015

AbstractA middle‐aged man received a kidney transplant from a deceased multi‐organ donor. The recipient suffered cardiac arrest several days post‐operatively and sustained hypoxic brain injury and was declared brain dead. Following the family's consent, the allograft kidney was retrieved and re‐transplanted into a man with end‐stage renal failure secondary to reflux nephropathy. The liver was not transplanted due to suspicion of fatty changes based on macroscopic appearance. After transplantation of other organs, liver histology revealed coagulative parenchymal necrosis with nuclear inclusions and moderate parenchymal cholestasis, suggestive of herpes viral hepatitis. Renal implantation biopsy showed histiocytes with enlarged nuclei containing viral inclusions in the capsular fibrous tissue, with positive immunostaining for herpes simplex virus (HSV). Anti‐viral therapy was commenced immediately after obtaining histological evidence of donor HSV infection. Our recipient had pre‐formed immunoglobulin G antibodies to HSV‐1 and HSV‐2, and was immunoglobulin M negative pre‐transplant. HSV viraemia was detected day 5 post‐transplant with a viral load of 7688 copies/mL by polymerase chain reaction assay. The recipient completed a 30 day course of intravenous ganciclovir before switching to oral valganciclovir as standard cytomegalovirus prophylaxis. The HSV polymerase chain reaction became undetectable on day 7 of intravenous ganciclovir and has remained undetectable. The patient remains well 9 months post‐transplant with an estimated glomerular filtration rate of 61 mL/min per 1.73 m2. Although renal allograft re‐use has been shown to be technically possible with a good outcome in this recipient, this does raise issues including assessment of allografts that have undergone repeated severe ischaemic insults and the potential of transmission of infections.
Associations between sex and incident chronic kidney disease in a prospective diabetic cohort
Authors: Yu Margaret K , Katon Wayne , Young Bessie A 
Published: March 2015

AbstractAimWomen with diabetes have a higher prevalence of chronic kidney disease (CKD) risk factors compared with men, but whether they are at higher risk for incident CKD remains uncertain.MethodsThis was a prospective, observational cohort study of 1464 patients with diabetes and normal renal function, recruited from primary care clinics at a vertically integrated healthcare system in Seattle, WA, USA. The primary predictor was sex. Incident CKD was defined by an estimated glomerular filtration rate (eGFR) <60 mL/min per 1.73 m2 by Chronic Kidney Disease‐Epidemiology equations or sex‐specific microalbuminuria (urine albumin/creatinine ratio ≥25 mg/g for women or ≥17 mg/g for men).ResultsOf the 1464 patients (52.0% women), CKD incidence rates were 154.0 and 144.3 cases per 1000 patient‐years for women and men, respectively. In the competing risks regression, women had an increased risk of incident CKD (sub‐hazard ratio 1.37, 95% confidence interval (CI) 1.17, 1.60) compared with men after adjustment for demographics, baseline eGFR and duration of diabetes, which persisted after additional adjustment for CKD risk factors, depressive symptoms and diabetes self‐care (sub‐hazard ratio 1.35, 95% CI 1.15, 1.59). Sex differences in incident CKD were consistent across age groups and appeared to be driven by differences in the development of low eGFR rather than microalbuminuria.ConclusionWomen with diabetes had a higher risk of incident CKD compared with men, which could not be entirely explained by differences in biologic CKD risk factors, depression or diabetes self‐care. Additional work is needed determine if these sex differences contribute to worse outcomes in women with diabetes.
Comparison of efficacy and safety between rabbit anti‐thymocyte globulin and anti‐T lymphocyte globulin in kidney transplantation from donation after cardiac death: A retrospective cohort study
Authors: Chen Guo‐Dong , Lai Xing‐Qiang , Ko Dicken Shiu‐Chung , Qiu Jiang , Wang Chang‐Xi , Han Ming , Li Jun , Huang Gang , He Xiao‐Shun , Chen Li‐Zhong 
Published: March 2015

AbstractAimTo compare the efficacy and safety between rabbit anti‐thymocyte globulin (Thymoglobulin) and anti‐T lymphocyte globulin (ATG‐Fresenius, ATG‐F) in donation after cardiac death (DCD) kidney transplantation.MethodsWe retrospectively analyzed 255 cases of DCD kidney transplantation performed at our hospital from February 2007 to October 2013. The patients were divided into two groups based on their induction therapies with Thymoglobulin (n = 188) or ATG‐F (n = 67). Clinical data were collected and compared between the two groups.ResultsDelayed graft function (DGF) occurred in 36 (19.1%) patients in the Thymoglobulin group versus 17 (25.4%) patients in the ATG‐F group (P = 0.281). However, if we subgroup the patients with increased risk factors for DGF, the DGF rate was 9/40 (22.5%) in the Thymoglobulin group versus 9/16 (56.3%) in the ATG‐F group (P = 0.015). Duration of DGF was significantly shorter in the Thymoglobulin group (11.7 days vs. 16.1 days). The acute rejection rate was significantly lower in the Thymoglobulin group (9.6% vs. 19.4%, P = 0.035). One‐year graft and patient survival were both comparable between the Thymoglobulin and ATG‐F groups. The adjusted odds ratio of DGF was 4.283 (1.137–16.13) between the ATG‐F and Thymoglobulin groups in patients with increased risk factors for DGF.ConclusionCompared with ATG‐F, Thymoglobulin may reduce duration of DGF and acute rejection rate after DCD kidney transplantation. Moreover, Thymoglobulin significantly reduced DGF in patients with increased risk factors for DGF.
Chromosomal regions associated with thein vitroculture response of wheat (Triticum aestivumL.) microspores
Authors: Nielsen Nanna H. , Andersen Stig U. , Stougaard Jens , Jensen Anni , Backes Gunter , Jahoor Ahmed 
Published: March 2015

AbstractGeneration of doubled haploid plants is a powerful tool in breeding, as homozygous individuals will be obtained directly from hybrids. However, genotype variability in regeneration efficiency of most European wheat (Triticum aestivumL.) varieties has limited its use in wheat. This study intended to identify quantitative trait loci (QTLs) for green plantlet regeneration from wheat microspore cultures. AQTLanalysis usingDArTmarkers was conducted based on a bi‐parental F3population, derived from a cross between the varieties Svilena and Jensen, which displayed markedly different capacity for plantlet regeneration. TwoQTLs on chromosome 1B and 7B explained 53% of the variation in green plantlet regeneration. Furthermore, a collection of 94 European wheat varieties was genotyped and phenotyped. The microspore response level was low among western and northern European wheat varieties, and the positiveQTLs found in the bi‐parental population were rare in the variety collection. Identification of the twoQTLs enables introduction of high regeneration efficiency into wheat germplasm. Moreover, our results proved that the efficient regeneration observed for one variety could be crossed into modern winter wheat.
Genetic diversity analysis of Moroccan lentil (Lens culinaris Medik.) landraces using Simple Sequence Repeat and Amplified Fragment Length Polymorphisms reveals functional adaptation towards agro‐environmental origins
Authors: Idrissi Omar , Udupa Sripada M. , Houasli Chafika , De Keyser Ellen , Van Damme Patrick , De Riek Jan 
Published: March 2015

AbstractIn the absence of previous molecular characterization, we assessed genetic diversity of 53 Moroccan lentil landraces including two local cultivars using simple sequence repeat (SSR) and amplified fragment length polymorphisms (AFLP). Nineteen SSRs yielded 213 alleles, and seven AFLP primer combinations gave 766 fragments of which 422 were polymorphic. Moderate to high genetic variation was observed. Several small groups of landraces were differentiated. Interestingly, one of the smallest groups contained short‐cycle landraces with high early vegetative growth. Landraces in that group were from the dry land location of Abda, where they were likely selected for adaptation to drought and heat stress over centuries. Another group contained two landraces from highland areas that may have been selected for specific adaptation to cold stress. A third group contained one landrace from the Zear region known for its seed quality and has been proposed for the protected designation of origin (PDO) quality mark. Both techniques gave evidence of differentiation of the latter landrace supporting the idea of PDO attribution. Functional grouping according to agro‐environmental origins, cycle duration and early vegetative vigour was observed.