bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellite markers of genetic diversity and population structure of Carica papaya
Authors: Matos E.L.S. , Oliveira E.J. , Jesus O.N. , Dantas J.L.L. 
Published: July 2013

AbstractWe assessed the genetic diversity of 96 papaya accessions by molecular characterisation using microsatellite markers. Fifteen polymorphic primers were selected. Accessions, which were classified as Common, Formosa and Solo according to fruit types, were evaluated for allele frequency, heterozygosity, polymorphism information content (PIC), inbreeding coefficient (f) and the genetic diversity structure. Fifteen primers amplified 68 alleles with an average of 4.53 per locus. PIC values ranged from 0.19 to 0.69. The observed heterozygosity (HO) was low for all selected microsatellites. High f estimates (0.58) and excess of homozygotes indicated inbreeding, mainly caused by the tendency to select hermaphrodite plants for succeeding generations. Analysis of molecular variance showed that most of the variation (98%) resides within subpopulation. The genetic analysis based on Bayesian statistics proved to be sensitive enough to detect relationships among the papaya accessions, grouping them into six clusters, irrespective of their classification types.
Genome‐wide in silico screening for microRNA genetic variability in livestock species
Authors: Jevsinek Skok D. , Godnic I. , Zorc M. , Horvat S. , Dovc P. , Kovac M. , Kunej T. 
Published: July 2013

SummaryMicroRNAs are a class of non‐coding RNAs that post‐transcriptionally regulate target gene expression. Previous studies have shown that microRNA gene variability can interfere with its function, resulting in phenotypic variation. Polymorphisms within microRNA genes present a source of novel biomarkers for phenotypic traits in animal breeding. However, little is known about microRNA genetic variability in livestock species, which is also due to incomplete data in genomic resource databases. Therefore, the aim of this study was to perform a genome‐wide in silico screening of genomic sources and determine the genetic variability of microRNA genes in livestock species using mirna sniper 3.0 (http://www.integratomics-time.com/miRNA-SNiPer/), a new version of our previously developed tool. By examining Ensembl and miRBase genome builds, it was possible to design a tool‐based generated search of 16 genomes including four livestock species: pig, horse, cattle and chicken. The analysis revealed 65 polymorphisms located within mature microRNA regions in these four species, including 28% within the seed region in cattle and chicken. Polymorphic microRNA genes in cattle and chicken were further examined for mapping to quantitative trait loci regions associated with production and health traits. The developed bioinformatics tool enables the analysis of polymorphic microRNA genes and prioritization of potential regulatory polymorphisms and therefore contributes to the development of microRNA‐based biomarkers in livestock species. The assembled catalog and the developed tool can serve the animal science community to efficiently select microRNA SNPs for further quantitative and molecular genetic evaluations of their phenotypic effects and causal associations with livestock production traits.
Participatory and evidence‐based recommendations for urban redevelopment following natural disasters: Older adults as policy advisers
Authors: Annear Michael , Keeling Sally , Wilkinson Tim 
Published: July 2013

AimTo develop community‐generated recommendations to inform urban environmental remediation following earthquakes in Christchurch, New Zealand, and share these with local decision‐makers during a participatory action research process.MethodsThis study employed three focus group discussions to critique mixed‐methods and multiphase results and develop evidence‐based recommendations. Participants included 30 volunteers and 8 knowledgeable advisers aged 65 years and older.ResultsParticipant recommendations addressed the remediation of earthquake‐affected suburbs, access to transportation, age‐friendly design, safer communities, resilient support agencies, and restoration of resources for social and cultural activities.ConclusionOlder collaborators identified salient barriers to active ageing and options for post‐earthquake redevelopment that had not previously been considered in research or policy. Independently living older adults are well placed to work with researchers to develop recommendations to improve the urban environment following natural disasters as well as in times of relative stability.
Effects of the estrous cycle on the efficacy of oocyte collection and in vitro embryo production in Duroc‐breed
Authors: Misumi Koji , Hirayama Yuri , Suzuki Misae , Nakai Michiko , Noguchi Junko , Kaneko Hiroyuki , Kikuchi Kazuhiro 
Published: July 2013

AbstractCollection efficacy and in vitro embryo developmental ability of oocytes obtained from Duroc‐breed ovary donors at different stages of the estrous cycle (days 6, 12 and 16 after estrus) were performed. The numbers of collected oocytes did not differ significantly among the different estrous cycle groups (total 72–90 oocytes per gilt). However, the blastocyst rates of oocytes collected on days 12 and 16 (9.2% and 19.4%, respectively) were significantly higher than those on day 6 (1.1%). More oocytes were obtained on day 16 from small follicles (<2 mm in diameter; 85.3 oocytes per gilt) than from medium‐sized (≥2–<6 mm) and large (≥6 mm) follicles (17.5 and 12.8 oocytes, respectively). The blastocyst rates in both the medium‐sized and large follicle groups (20.0% and 19.2%, respectively) were significantly higher than that in the small follicle group (6.3%). The blastocyst cell numbers in both the medium‐sized and large follicle groups (39.4 and 43.3 cells, respectively) were significantly higher than that in the small follicle group (30.6 cells). The results suggest that oocyte collection from cycling Duroc pigs can be carried out efficiently from the late luteal to follicular stage. Those oocytes collected from medium‐sized and large follicles show better embryo development.
Correspondence in forest species composition between the Vegetation Map of Africa and higher resolution maps for seven African countries
Authors: Kindt Roeland , Lillesø Jens‐Peter B. , van Breugel Paulo , Bingham Michael , Demissew Sebsebe , Dudley Cornell , Friis Ib , Gachathi Francis , Kalema James , Mbago Frank , Moshi Heriel N. , Mulumba John W. , Namaganda Mary , Ndangalasi Henry J. , Ruffo Christopher K. , Minani Védaste , Jamnadass Ramni H. , Graudal Lars 
Published: July 2013

AbstractQuestionHow well does the forest classification system of the 1:5,000,000 vegetation map of Africa developed by Frank White correspond with classification systems and more extensive information on species assemblages of higher resolution maps developed for Ethiopia, Kenya, Malawi, Rwanda, Tanzania, Uganda and Zambia?MethodsWe reviewed various national and sub‐national vegetation maps for their potential in increasing the resolution of the African map. Associated documentation was consulted to compile species assemblages, and to identify indicator species, for national forest vegetation types. Indicator species were identified for each regional forest type by selecting those species that, among all the species listed for the same phytochorion (regional centre of endemism), were listed only for that forest type. For each of the national forest types, we counted the number of indicator species of the anticipated regional type. Floristic relationships (expressed by four different ecological distance measures) among national forest types were investigated based on distance‐based redundancy analysis, permutational multivariate analysis of variance (PERMANOVA) using distance matrices and hierarchical clustering.ResultsFor most of the national forests, the analysis of indicator species and floristic relationships confirmed the regional classification system for the majority of national forest types, including the allocation to different phytochoria. Permutation tests confirmed allocation of national forest types to regional typologies, although the number of possible permutations limited inferences for the Zambezian and Lake Victoria phytochoria. Two forest types from Ethiopia and Kenya did not correspond to regional forest types.&#4;ConclusionsOur analysis provides support that as the classification systems are compatible, the resolution and information content of the vegetation map of Africa can be directly improved by adding information from national maps, probably leading to improved liability of its application domains. We found statistical evidence for a distinct Afromontane phytochorion. We suggest expanding the regional forest classification system with ‘Afromontane moist transitional forest’. Among the various application domains of the higher resolution maps, these maps allow for an enhanced phytochoristic analysis of eastern Africa.
Impact of psychotropic drugs on suicide and suicidal behaviors
Authors: Yerevanian Boghos I , Choi Young Mee 
Published: July 2013

ObjectiveTo examine the impact of psychotropic drugs on suicide and suicidal behaviors in bipolar disorders.MethodsA Medline search of articles published from January 1960 to January 2013 was performed using relevant keywords to identify studies examining the relationship of psychotropic drugs to suicidal behaviors. The publications were further reviewed for relevant references and information. Additionally, the US Food and Drug Administration Center for Drug Evaluation Research website was searched.ResultsThe available studies used differing methodologies, making interpretation of the findings difficult. Studies suggest that antidepressants may increase suicidal risk in bipolar disorder, this possibly being related to the induction of broadly defined mixed states. There is no evidence that antiepileptic drugs as a class increase suicidal risk in patients with bipolar disorder. Only lithium provides convincing data that it reduces the risk of suicide over the long term. There is little known regarding the effects of antipsychotics, as well as anti‐anxiety and hypnotic drugs, on suicidal behavior.ConclusionsThe available evidence for the impact of psychotropics on suicidal risk in patients with bipolar disorder is largely methodologically flawed and, except for a few instances, clinically not useful at this point. Adequately powered, prospective randomized controlled studies are needed to assess the impact of each class of psychotropic and each psychotropic as well as common combination therapies. Until such studies have been carried out, clinicians are urged to exercise caution in using these drugs and rely on the traditional means of carefully assessing and monitoring patients with bipolar disorder who are at high risk for suicide.
Biallelic losses of 13q do not confer a poorer outcome in chronic lymphocytic leukaemia: analysis of 627 patients with isolated 13q deletion
Authors: Puiggros Anna , Delgado Julio , Rodriguez‐Vicente Ana , Collado Rosa , Aventín Anna , Luño Elisa , Grau Javier , Hernandez José Ángel , Marugán Isabel , Ardanaz Maite , González Teresa , Valiente Alberto , Osma Mar , Calasanz Maria José , Sanzo Carmen , Carrió Ana , Ortega Margarita , Santacruz Rodrigo , Abrisqueta Pau , Abella Eugènia , Bosch Francesc , Carbonell Félix , Solé Francesc , Hernández Jesús Maria , Espinet Blanca ,   Grupo Cooperativo Español de Citogenética Hematológica (GCECGH) and Grupo Español de Leucemia Linfática Crónica (GELLC).
Published: July 2013

SummaryLosses in 13q as a sole abnormality confer a good prognosis in chronic lymphocytic leukaemia (CLL). Nevertheless, its heterogeneity has been demonstrated and the clinical significance of biallelic 13q deletions remains controversial. We compared the clinico‐biological characteristics of a series of 627 patients harbouring isolated 13q deletions by fluorescence in situ hybridization (FISH), either monoallelic (13q × 1), biallelic (13q × 2), or the coexistence of both clones (13qM). The most frequent 13q deletion was 13q × 1 (82·1%), while 13q × 2 and 13qM represented 8·6% and 9·3% of patients respectively. The median percentage of altered nuclei significantly differed across groups: 55%, 72·5% and 80% in 13q × 1, 13q × 2 and 13qM (P < 0·001). However, no significant differences in the clinical outcome among 13q groups were found. From 84 patients with sequential FISH studies, eight patients lost the remaining allele of 13q whereas none of them changed from 13q × 2 to the 13q × 1 group. The percentage of abnormal cells detected by FISH had a significant impact on the five‐year cumulative incidence of treatment and the overall survival, 90% being the highest predictive power cut‐off. In conclusion, loss of the remaining 13q allele is not enough to entail a worse prognosis in CLL. The presence of isolated 13q deletion can be risk‐stratified according to the percentage of altered cells.
Prostate‐specific antigen doubling time as a progression criterion in an active surveillance programme for patients with localized prostate cancer
Authors: Thomsen Frederik Birkebæk , Christensen Ib Jarle , Brasso Klaus , Røder Martin Andreas , Iversen Peter 
Published: July 2013

Objectives
To elucidate the role of prostate‐specific antigen (PSA) doubling time (PSAdt) as a progression criterion in patients with low‐risk prostate cancer managed by active surveillance (AS).
To assess the correlation between PSAdt during AS and final histopathology after radical prostatectomy (RP) in patients meeting predefined progression criteria.
Patients and Methods
A total of 258 consecutive patients on an AS programme were included in the study.
The PSAdt was calculated in patients with two or more PSA values, and 95% confidence intervals (CIs) were calculated in patients with four or more PSA values.
Progression risk groups were defined as follows: high‐risk: PSAdt <3 years, rebiopsy Gleason score (GS) ≥4 + 3, more than three positive biopsy cores, and/or bilateral tumour or cT ≥2c disease; intermediate‐risk: PSAdt 3–5 years, GS = 3 + 4 or cT2b disease; and low‐risk: PSAdt >5 years, without histopathological or clinical progression.
Definitive treatment was recommended for patients in the high‐risk group and treatment options were discussed with those in the intermediate‐risk group.
Results
A total of 2291 PSA values obtained during AS were available, of which 2071 were considered valid in the 258 patients.
PSAdt values with 95% CIs were calculated in 221 patients based on a median of 8 PSA values.
The 95% CIs for PSAdt overlapped considerably and in up to 91% of the patients, the 95% CIs overlapped among the risk group definitions.
A total of 26% (68/258 patients) underwent RP after meeting the progression criteria.
There was no association between preoperative PSAdt and final histopathology (P = 0.87).
Conclusion
The uncertainty of calculated PSAdt during AS leads to a significant risk of patients being misclassified in terms of risk of progression, which limits the use of PSAdt in the management of patients on AS.
Assessment of Leishmanicidal and Trypanocidal Activities of Aliphatic Diamine Derivatives
Authors: Yamanaka Celina N. , Giordani Raquel B. , Rezende Celso O. , Eger Iriane , Kessler Rafael L. , Tonini Maiko L. , de Moraes Milene H. , Araújo Debora P. , Zuanazzi Jose A. , de Almeida Mauro V. , Steindel Mario 
Published: July 2013

Leishmanicidal and trypanocidal activity of seventeen lipophilic diamines was evaluated in vitro against Leishmania braziliensis, L. chagasi, and Trypanosoma cruzi. Twelve compounds presented anti‐Leishmania and six showed anti‐T. cruzi amastigote activity. Compound 14 (N‐tetradecyl‐1,4‐butanediamine) was the most active against both L. braziliensis (IC50 = 2.6 μm) and L. chagasi (IC50 = 3.0 μm) which showed a selectivity index (SI) >100. N‐decyl‐1,6‐hexanediamine (compound 9) presented an IC50 = 1.6 μm and SI >187 and was over six times more potent than the reference drug benznidazole against T. cruzi. Treatment of infected or uninfected macrophages with compounds 9 and 14 did not induce significant TNFα and NO production. Four compounds (15, 16, 22, and 23) inhibited 78.9%, 77.7%, 83.7%, and 70.1% of rTRLb activity, respectively, and compound 23 inhibited 73.3% of rTRTc activity at 100 μm. A concentration‐dependent effect on mitochondrial membrane depolarization was observed in T. cruzi epimastigotes treated with compound 9, suggesting this mechanism may be involved in the trypanocidal effect. On the contrary, in L. braziliensis promastigotes treated with compound 14, no mitochondrial depolarization was observed. Our results demonstrate that N‐decyl‐1,6‐hexanediamine and N‐tetradecyl‐1,4‐butanediamine are promising molecules for the development of novel leading compounds against T. cruzi and Leishmania spp., particularly given a possible alternative mechanism of action.
Epidemiological associations of allergy, IgE and cancer
Authors: Josephs D. H. , Spicer J. F. , Corrigan C. J. , Gould H. J. , Karagiannis S. N. 
Published: July 2013

SummarySeveral epidemiological studies have evaluated potential associations between allergy and risk of malignancy. It remains clear that the relationship between allergy and cancer is complex. Three hypotheses have been proposed to account for observed relationships: these are chronic inflammation, immunosurveillance, prophylaxis, and we propose adding a fourth: inappropriate T‐helper 2 (Th2) immune skewing. Each of these attempts to explain either the increased or decreased risk of different cancer types in ‘allergic’ patients reported in the literature. All four hypotheses are based on known mechanisms of allergic inflammation and/or IgE antibody functions, and uphold the view of an immunological basis for the relationship between allergy and malignancies. This review summarizes and draws conclusions from the epidemiological literature examining the relationships between specific types of cancer and allergic diseases. Particular emphasis is placed on the most recent contributions to the field, and on consideration of the allergic immune mechanisms that may influence positive or negative associations.
Retinoic acid-producing,ex-vivo-generated human tolerogenic dendritic cells induce the proliferation of immunosuppressive B lymphocytes
Authors: Di Caro V , Phillips B , Engman C , Harnaha J , Trucco M , Giannoukakis N 
Published: July 2013

SummaryWhile much is known about tolerogenic dendritic cell effects on forkhead box protein 3 (FoxP3)+ regulatory T cells, virtually nothing is known about their effects on another arm of immunoregulation that is mediated by a subpopulation of immunosuppressive B cells. These cells suppress rheumatoid arthritis, lupus and inflammatory bowel disease in mice, and functional defects have been reported in human lupus. We show that co-stimulation-impaired tolerogenic dendritic cells that prevent and reverse type 1 diabetes mellitus induce the proliferation of human immunosuppressive B cells in vitro. We also show that the suppressive properties of these B cells concentrate inside the CD19+CD24+ B cell population and more specifically inside the CD19+CD24+CD38+ regulatory B cell population. We discovered that B cell conversion into suppressive cells in vitro is partially dependent on dendritic cell production of retinoic acid and also that CD19+CD24+CD38+ B regulatory cells express retinoic acid receptors. Taken together, our data suggest a model whereby part of the immunosuppressive properties of human tolerogenic dendritic cells could be mediated by retinoic acid which, in addition to its known role in favouring T cell differentiation to FoxP3+ regulatory T cells, acts to convert B cells into immunosuppressive cells.
Transforming growth factor (TGF)-β signalling is increased in rheumatoid synovium but TGF-β blockade does not modify experimental arthritis
Authors: Gonzalo-Gil E , Criado G , Santiago B , Dotor J , Pablos J L , Galindo M 
Published: July 2013

SummaryThe aim of this study was to analyse the distribution of regulatory and inhibitory mothers against decapentaplegic homologue (Smad) proteins as markers of active transforming growth factor (TGF)-β signalling in rheumatoid arthritis (RA) synovial tissue and to investigate the effect of TGF-β blockade in the development and progression of collagen-induced arthritis. The expression of Smad proteins in synovial tissues from RA, osteoarthritic and healthy controls was analysed by immunohistochemistry. Arthritis was induced in DBA/1 mice by immunization with chicken type-II collagen (CII). TGF-β was blocked in vivo with the specific peptide p17 starting at the time of immunization or on the day of arthritis onset. T cell population frequencies and specific responses to CII were analysed. The expression of cytokines and transcription factors was quantified in spleen and joint samples. Statistical differences between groups were compared using the Mann–Whitney U-test or one-way analysis of variance (anova) using the Kruskal–Wallis test. p-Smad-2/3 and inhibitory Smad-7 expression were detected in RA and control tissues. In RA, most lymphoid infiltrating cells showed nuclear p-Smad-2/3 without Smad-7 expression. Treatment with TGF-β antagonist did not affect clinical severity, joint inflammation and cartilage damage in collagen-induced arthritis. Frequency of T cell subsets, mRNA levels of cytokines and transcription factors, specific proliferation to CII, serum interleukin (IL)-6 and anti-CII antibodies were comparable in p17 and phosphate-buffered saline (PBS)-treated groups. The pattern of Smad proteins expression demonstrates active TGF-β signalling in RA synovium. However, specific TGF-β blockade does not have a significant effect in the mice model of collagen-induced arthritis.
Intraperitoneal insulin delivery to patients with type 1 diabetes results in higher serum IGF‐I bioactivity than continuous subcutaneous insulin infusion
Authors: Hedman Christina A. , Frystyk Jan , Lindström Torbjörn , Oskarsson Per , Arnqvist Hans J. 
Published: July 2013

SummaryObjectiveType 1 diabetes (T1D) is associated with low IGF‐I and altered levels of IGF‐binding proteins (IGFBPs) in plasma. This may be of importance for insulin sensitivity and the risk of developing diabetic complications. We hypothesized that IGF‐I bioactivity is affected by the route of insulin administration and that continuous intraperitoneal insulin infusion (CIPII) has a more pronounced effect than continuous subcutaneous insulin infusion (CSII).Design and methodsWe compared 10 patients with T1D on CIPII with 20 age‐ and sex‐matched patients on CSII. Blood sampling was carried out 7–9 am after an overnight fast. All patients were C‐peptide negative. IGF‐I bioactivity was measured in vitro using a specific IGF‐I kinase receptor activation (KIRA) assay. IGF‐I was also measured by immunoassay together with IGF‐II, IGFBP‐1 and IGFBP‐2.ResultsWhen compared with subcutaneous insulin, intraperitoneal insulin resulted in (CIPII vs CSII) higher IGF‐I bioactivity (1·83 ± 0·76 vs 1·16 ± 0·24 μg/l; P = 0·02), IGF‐I (120 ± 35 vs 81 ± 19 μg/l; P = 0·01) and IGF‐II (1050 ± 136 vs 879 ± 110 μg/l; P = 0·02). By contrast, log‐transformed IGFBP‐1 was reduced (P = 0·013), whereas log‐transformed IGFBP‐2 was not different (P = 0·12). There was a positive correlation between IGF bioactivity and IGF‐I (r = 0·69; P < 0·001) and an inverse correlation between IGF‐I bioactivity and log10 IGFBP‐1 (r = −0·68, P < 0·001).ConclusionThe in vitro IGF‐I bioactivity was higher in patients treated with CIPII compared with CSII supporting the theory that the route of insulin administration is of importance for the activity of the IGF system. Intraperitoneal insulin administration may therefore be beneficial by correcting the alterations of the IGF system in T1D.