True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. ...Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
The identification and proper naming of microfungi, in particular plant, animal and human pathogens, remains challenging. Molecular identification is becoming the default approach for many fungal ...groups, and environmental metabarcoding is contributing an increasing amount of sequence data documenting fungal diversity on a global scale. This includes lineages represented only by sequence data. At present, these taxa cannot be formally described under the current nomenclature rules. By considering approaches used in bacterial taxonomy, we propose solutions for the nomenclature of taxa known only from sequences to facilitate consistent reporting and communication in the literature and public sequence repositories.
Improving survival of retinoblastoma in Uganda Waddell, Keith M; Kagame, Kenneth; Ndamira, Andrew ...
British journal of ophthalmology,
07/2015, Letnik:
99, Številka:
7
Journal Article
Recenzirano
Odprti dostop
Diagnostic delay results in relatively high mortality among children with retinoblastoma in Uganda, where treatment was limited to surgery and, for some, radiotherapy. In order to improve outcomes, a ...simple programme of neoadjuvant and adjuvant chemotherapy was introduced. Here we report survival before and after this change to medical practice.
Affordable standard off-patent chemotherapy agents were administered by trained paramedical staff to groups of patients at the same time. Survival before and after the introduction of chemotherapy was monitored. Between 2006 and 2013 a total of 270 patients with retinoblastoma were included, 181 treated prior to chemotherapy and 89 after (beginning in 2009). We had 94% follow-up and 249 had histological verification of diagnosis.
Using a proportional hazards model adjusted for age, sex and laterality, children treated after chemotherapy was introduced had a 37% lower risk of dying (HR 0.63, 95% CI 0.41 to 0.99) compared with children treated before. Prior to the introduction of chemotherapy only 15% of children who survived bilateral disease retained vision after treatment compared with 71% after chemotherapy.
The introduction of chemotherapy proved safe and cost-effective in non-specialist hands and was associated with significant improvements in survival and, among bilateral cases, in preserving vision.
A second genus in Chlorociboriaceae is described here as
Brahmaculus
gen. nov.
Macroscopically distinctive, all species have bright yellow apothecia with several apothecial cups held on short ...branches at the tip of a long stipe. The genus is widely distributed across the Southern Hemisphere; the four new species described here include two from Chile (
B. magellanicus
sp. nov.
,
B. osornoensis
sp. nov.
) and one each from New Zealand (
B. moonlighticus
sp. nov.
) and Australia (
B. packhamiae
sp. nov.
). They differ from species referred to
Chlorociboria
, the only other genus in Chlorociboriaceae, in their terrestrial habitat and ascomata that are noticeably more hairy than the known
Chlorociboria
species, most of which have apothecia with short, macroscopically indistinct hair-like elements. Based on our analyses,
Chlorociboria
as accepted here is paraphyletic. Additional study is needed to clarify where alternative, monophyletic generic limits should be drawn and how these genera may be recognised morphologically. Also described here are three new
Chlorociboria
spp. from New Zealand (
C. metrosideri
sp. nov.
,
C. solandri
sp. nov.
,
C. subtilis
sp. nov.
), distinctive in developing on dead leaves rather than wood and in two of them not forming the green pigmentation characteristic of most
Chlorociboria
species. New Zealand specimens previously incorrectly identified as
Chlorociboria argentinensis
are provided with a new name,
C. novae-zelandiae
sp. nov.
To characterise the clinical features, treatment and outcome of children diagnosed with retinoblastoma in Uganda.
The study comprised a 6-year nationwide enrolment with follow-up.
In total, 282 cases ...were enrolled, 26% (72) were bilateral; 6% were lost to follow-up. Almost all diagnoses in the first affected eye were International Classification of Retinoblastoma group E or worse. Histology was available for 92%; of those, 45%, had extraocular tumour at diagnosis. Enucleation of the first eye was done for 271; 94 received radiotherapy to the socket and in the last 2 years, 70 children received chemotherapy. At close of study, 139 children had died. Survival, as determined in a proportional hazards model adjusted for age, sex, laterality and treatment era (pre or post introduction of chemotherapy), varied by extent of the tumour (p<0.001); children with only intraocular involvement were 80% less likely to die (HR=0.21, 95% CI 0.12 to 0.35) compared with children with extraocular involvement.
Diagnostic delay results in relatively high mortality among children with retinoblastoma in Uganda. There is an urgent need for more effective treatment modalities, particularly chemotherapy, and nationwide efforts to encourage earlier access to medical care.
Abstract Objectives The disconfirmation model hypothesizes that satisfaction is a function of a perceived discrepancy from an initial expectation. Our objectives were: (1) to test the disconfirmation ...model as it applies to patient satisfaction with waiting time (WT) and (2) to build an explanatory model of the determinants of satisfaction with WT for hip and knee replacement. Methods We mailed 1000 questionnaires to 2 random samples: patients waiting or those who had received a joint replacement within the preceding 3–12 months. We used ordinal logistic regression analysis to build an explanatory model of the determinants of satisfaction. Results Of the 1330 returned surveys, 1240 contained patient satisfaction data. The sample was 57% female; mean age was 70 years (SD 11). Consistent with the disconfirmation model, when their WTs were longer than expected, both waiting (OR 5.77, 95% CI 3.57–9.32) and post-surgery patients (OR 6.57, 95% CI 4.21–10.26) had greater odds of dissatisfaction, adjusting for the other variables in the model. Compared to those who waited 3 months or less, post-surgery patients who waited 6 to 12 months (OR 2.59, 95% CI 1.27–5.27) and over 12 months (OR 3.30, 95% CI 1.65–6.58) had greater odds of being dissatisfied with their waiting time. Patients who felt they were treated unfairly had greater odds of being dissatisfied (OR 4.74, 95% CI 2.60–8.62). Conclusions In patients on waiting lists and post-surgery for hip and knee replacement, satisfaction with waiting times is related to fulfillment of expectations about waiting, as well as a perception of fairness. Measures to modify expectations and increase perceived fairness, such as informing patients of a realistic WT and communication during the waiting period, may increase satisfaction with WTs.
Background Mesocosm experiments have become increasingly popular in climate change research as they bridge the gap between small-scale, less realistic, microcosm experiments, and large-scale, more ...complex, natural systems. Characteristics of aquatic mesocosm designs (e.g., mesocosm volume, study duration, and replication) vary widely, potentially affecting the magnitude and direction of effect sizes measured in experiments. In this global systematic review we aim to identify the type, direction and strength of climate warming effects on aquatic species, communities and ecosystems in mesocosm experiments. Furthermore, we will investigate the context-dependency of the observed effects on several a priori determined effect moderators (ecological and methodological). Our conclusions will provide recommendations for aquatic scientists designing mesocosm experiments, as well as guidelines for interpretation of experimental results by scientists, policy-makers and the general public. Methods We will conduct a systematic search using multiple online databases to gather evidence from the scientific literature on the effects of warming experimentally tested in aquatic mesocosms. Data from relevant studies will be extracted and used in a random effects meta-analysis to estimate the overall effect sizes of warming experiments on species performance, biodiversity and ecosystem functions. Experimental characteristics (e.g., mesocosm size and shape, replication-level, experimental duration and design, biogeographic region, community type, crossed manipulation) will be further analysed using subgroup analyses. Keywords: Climate change, Global warming, Mesocosm, Microcosm, Aquatic, Marine, Estuarine, Freshwater, Experimental design, Methodology
Objectives To obtain patients’ perspectives on acceptable waiting times for hip or knee replacement surgery.
Methods A questionnaire with both open‐ and close‐ended items was mailed to 432 ...consecutive patients who had hip or knee replacement surgery 3–12 months previously in Saskatchewan, Canada. A content analysis was used to analyse the text data from the open‐ended questions.
Results The sample of 303 (response rate 70%) was 59% female with a mean age of 70 years (SD 11). The median waiting time from the decision date to surgery was 17 weeks. Individuals who rated their waiting time very acceptable (48%) had a median waiting time of 13 weeks compared with a median waiting time of 22 weeks for those who rated it unacceptable (23%). The two most common determinants of acceptability were patient expectations and pain and its impact on patient quality of life. The median maximum acceptable waiting time was 13 weeks and median ideal waiting time, 8.6 weeks. Seventy‐nine per cent felt that those in greater need (higher severity) should go before them on the waiting list. Patient ratings of maximum acceptable waiting time were based on: pain and loss of mobility, time needed to prepare for surgery, and severity at the time of seeing the surgeon. In consideration of changing their surgeon to one with a shorter waiting list, 68% would not.
Conclusions Patient views on waiting times are not only related to quality of life issues, but also to prior expectations and notions of fairness and priority. Understanding patient views on waiting for surgery has implications for better management of waiting times and experiences for joint replacement.
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