The tree of one percent.
Ontology highlight
ABSTRACT:
SUBMITTER: Dagan T
PROVIDER: S-EPMC1794558 | biostudies-literature | 2006
REPOSITORIES: biostudies-literature
Publications
Two significant evolutionary processes are fundamentally not tree-like in nature--lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes. To incorporate such processes into the bigger picture of early evolution, biologists need to depart from the preconceived notion that all genomes are related by a single bifurcating tree. ...[more]
Similar Datasets
Project description:A scalable quantum computer could be built by networking together many simple processor cells, thus avoiding the need to create a single complex structure. The difficulty is that realistic quantum links are very error prone. A solution is for cells to repeatedly communicate with each other and so purify any imperfections; however prior studies suggest that the cells themselves must then have prohibitively low internal error rates. Here we describe a method by which even error-prone cells can perform purification: groups of cells generate shared resource states, which then enable stabilization of topologically encoded data. Given a realistically noisy network (?10% error rate) we find that our protocol can succeed provided that intra-cell error rates for initialisation, state manipulation and measurement are below 0.82%. This level of fidelity is already achievable in several laboratory systems.
| S-EPMC3644110 | biostudies-literature
Project description:This paper explores the trajectories of Norwegians who, in their late-thirties, possessed financial assets, such as securities, company shares and stocks, qualifying them as the wealthiest one percent nationally. We describe the accumulation of financial wealth over a 25-year period in adulthood and study how different wealth sequences are linked to family origins and kinship ties. Although some Norwegians manage to build up large fortunes from relatively modest starting points over their life courses, we find that the value of the assets possessed by self-made individuals, and their ability to retain wealth over time, differ significantly to those based on dynastic lineage. Among the latter group, profound wealth early in adulthood and strategic positions in the economy add to propel exponential ownership of financial wealth from a young age and throughout adulthood. This chimes with C. Wright Mills' suggestion that the amassing of great fortunes is driven by two mechanisms of the big jump that enables initial asset build-up, and the accumulation of advantages that flows from advantageous economic and social ties. Kinship seems of key importance to ensure the efficacy of both mechanisms. Differences in the relationship of wealth accumulation and class origin seem to have little to do with educational strategies. We draw attention to direct wealth transfers and the institution of marriage as two little explored dimensions involved in dynastic closure.
| S-EPMC9305140 | biostudies-literature
Project description:Forest structure is strongly related to forest ecology, and it is a key parameter to understand ecosystem processes and services. Airborne laser scanning (ALS) is becoming an important tool in environmental mapping. It is increasingly common to collect ALS data at high enough point density to recognize individual tree crowns (ITCs) allowing analyses to move beyond classical stand-level approaches. In this study, an effective and simple method to map ITCs, and their stem diameter and aboveground biomass (AGB) is presented. ALS data were used to delineate ITCs and to extract ITCs' height and crown diameter; then, using newly developed allometries, the ITCs' diameter at breast height (DBH) and AGB were predicted. Gini coefficient of DBHs was also predicted and mapped aggregating ITCs predictions. Two datasets from spruce dominated temperate forests were considered: one was used to develop the allometric models, while the second was used to validate the methodology. The proposed approach provides accurate predictions of individual DBH and AGB (R2 = .85 and .78, respectively) and of tree size distributions. The proposed method had a higher generalization ability compared to a standard area-based method, in particular for the prediction of the Gini coefficient of DBHs. The delineation method used detected more than 50% of the trees with DBH >10 cm. The detection rate was particularly low for trees with DBH below 10 cm, but they represent a small amount of the total biomass. The Gini coefficient of the DBH distribution was predicted at plot level with R2 = .46. The approach described in this work, easy applicable in different forested areas, is an important development of the traditional area-based remote sensing tools and can be applied for more detailed analysis of forest ecology and dynamics.
| S-EPMC6010772 | biostudies-literature
Project description:ObjectivesTo investigate women's understanding and attitudes towards the National Cervical Screening Program (NCSP) and to explore methods to improve screening participation.DesignSemi-structured face-to-face interviews were conducted through convenience and snowball sampling. Thematic analysis occurred using the interpretivist framework.SettingA private general practice in North Queensland.ParticipantsWomen between the ages of 18 and 74 who attended the general practice were eligible to participate. Fourteen women between 20 and 58 years old were interviewed.ResultsParticipants were concerned that the new NCSP would miss cancer due to longer screening intervals and reliance on primary human papilloma virus (HPV) testing. They believed that young women are at increased risk of cervical cancer, due to perceived HPV vaccine ineffectiveness and parent objection to vaccination. Most participants were not agreeable to self-sampling and preferred their doctor to perform screening. Personal and practitioner beliefs influenced a woman's screening participation. Personal factors include being healthy for themselves and their family, previous abnormal smears and family history of cancer. Emphasis was placed on feeling 'comfortable' with their practitioner which included patient rapport and gender preference. Proposed methods to improve cervical screening included education programmes, advertising campaigns, general practitioner interventions and improving accessibility.ConclusionsIt is apparent that women are hesitant about the new NCSP. However, when provided with additional information they were more amenable to the changes. This highlights the need to improve awareness of cervical screening and the new NCSP.
| S-EPMC7064076 | biostudies-literature
Project description:Researchers and educators have long wrestled with the question of how best to teach their clients be they humans, non-human animals or machines. Here, we examine the role of a single variable, the difficulty of training, on the rate of learning. In many situations we find that there is a sweet spot in which training is neither too easy nor too hard, and where learning progresses most quickly. We derive conditions for this sweet spot for a broad class of learning algorithms in the context of binary classification tasks. For all of these stochastic gradient-descent based learning algorithms, we find that the optimal error rate for training is around 15.87% or, conversely, that the optimal training accuracy is about 85%. We demonstrate the efficacy of this 'Eighty Five Percent Rule' for artificial neural networks used in AI and biologically plausible neural networks thought to describe animal learning.
| S-EPMC6831579 | biostudies-literature
Project description:BackgroundWhile full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets.ResultsWe found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences.ConclusionThese results demonstrate that partial gene sequences and gappy multiple sequence alignments can pose a major problem for phylogenetic analysis. The concern will be greatest for high-throughput phylogenomic analyses, in which Neighbor Joining is often the preferred method due to its computational efficiency. Both approaches can be used to increase the accuracy of phylogenetic inference from a gappy alignment. The choice between the two approaches will depend upon how robust the application is to the loss of sequences from the input set, with alignment masking generally giving a much greater improvement in accuracy but at the cost of discarding a larger number of the input sequences.
| S-EPMC2359737 | biostudies-literature
Project description:A one-step multiplex real-time reverse transcription polymerase chain reaction (RT-qPCR) based on TaqMan probes was developed for the simultaneous detection of Apple mosaic virus (ApMV), Apple stem pitting virus (ASPV) and Apple stem grooving virus (ASGV) in total RNA of pome trees extracted with a CTAB method. The sensitivity of the method was established using in vitro synthesized viral transcripts serially diluted in RNA from healthy, virus-tested (negative) pome trees. The three viruses were simultaneously detected up to a 10-4 dilution of total RNA from a naturally triple-infected apple tree prepared in total RNA of healthy apple tissue. The newly developed RT-qPCR assay was at least one hundred times more sensitive than conventional single RT-PCRs. The assay was validated with 36 field samples for which nine triple and 11 double infections were detected. All viruses were detected simultaneously in composite samples at least up to the ratio of 1:150 triple-infected to healthy pear tissue, suggesting the assay has the capacity to examine rapidly a large number of samples in pome tree certification programs and surveys for virus presence.
| S-EPMC5547701 | biostudies-literature
Project description:Street trees are an important component of green infrastructure in cities, providing multiple ecosystem services (ES) and hence contributing to urban resilience, sustainability and livability. Still, access to these benefits may display an uneven distribution across the urban fabric, potentially leading to socio-environmental inequalities. Some studies have analyzed the distributional justice implications of street tree spatial patterns, but generally without quantifying the associated ES provision. This research estimated the amount of air purification, runoff mitigation and temperature regulation provided by circa 200,000 street trees in Barcelona, Spain, using the i-Tree Eco tool. Results were aggregated at neighborhood (n = 73) and census tract (n = 1068) levels to detect associations with the distribution of five demographic variables indicating social vulnerability, namely: income, residents from the Global South, residents with low educational attainment, elderly residents, and children. Associations were evaluated using bivariate, multivariate and cluster analyses, including a spatial autoregressive model. Unlike previous studies, we found no evidence of a significant and positive association between the distribution of low income or Global South residents and a lower amount of street tree benefits in Barcelona. Rather, higher ES provision by street trees was associated with certain types of vulnerable populations, especially elderly citizens. Our results also suggest that street trees can play an important redistributive role in relation to the local provision of regulating ES due to the generally uneven and patchy distribution of other urban green infrastructure components such as urban forests, parks or gardens in compact cities such as Barcelona. In the light of these findings, we contend that just green infrastructure planning should carefully consider the distributive implications associated with street tree benefits.
| S-EPMC6855261 | biostudies-literature
Project description:Nasal reconstruction after skin cancer excision has routinely been challenging without any aesthetic sequelae, and any defects on the nose are readily noticeable. To circumvent this problem, surgeons have developed different flap techniques to mobilize adjacent tissue to repair aesthetically sensitive defects. We describe our experience, outcomes, and valuable tips for using the "tree flap," a novel modification of the hatchet flap that extends the back cut to significantly increase mobility, leaving only a small skin paddle to maintain perfusion to the flap. The combination of undermining, a rotatory component, and minimal skin attachment allows radical mobility without compromising blood supply. Thus, the tree flap allows for reconstruction of defects of the dorsum of the nose and defects near the nasal tip with ease, given both advancement and rotational movements. Compared with other local flaps such as the shark pedicle flap or bilobed flap, the tree flap has a similar learning curve, minimal donor site morbidity, and equivalent aesthetic outcome. It may be used to repair larger defects that may not be amenable to the bilobed flap as an alternative to a full-thickness skin graft. In our experience, the tree flap also has the advantage of a lower rate of pin cushioning when compared with other options such as the bilobed flap. The tree flap has great mobility and is a reliable option for reconstruction of the lower one-third of the nose with excellent aesthetic results and minimal complications.
| S-EPMC11018149 | biostudies-literature
Project description:BackgroundVery severe chronic obstructive pulmonary disease causes cor pulmonale with elevated pulmonary vascular resistance and secondary reductions in left ventricular filling, stroke volume, and cardiac output. We hypothesized that emphysema, as detected on computed tomography (CT), and airflow obstruction are inversely related to left ventricular end-diastolic volume, stroke volume, and cardiac output among persons without very severe lung disease.MethodsWe measured left ventricular structure and function with the use of magnetic resonance imaging in 2816 persons who were 45 to 84 years of age. The extent of emphysema (expressed as percent emphysema) was defined as the percentage of voxels below -910 Hounsfield units in the lung windows on cardiac computed tomographic scans. Spirometry was performed according to American Thoracic Society guidelines. Generalized additive models were used to test for threshold effects.ResultsOf the study participants, 13% were current smokers, 38% were former smokers, and 49% had never smoked. A 10-point increase in percent emphysema was linearly related to reductions in left ventricular end-diastolic volume (-4.1 ml; 95% confidence interval [CI], -3.3 to -4.9; P<0.001), stroke volume (-2.7 ml; 95% CI, -2.2 to -3.3; P<0.001), and cardiac output (-0.19 liters per minute; 95% CI, -0.14 to -0.23; P<0.001). These associations were of greater magnitude among current smokers than among former smokers and those who had never smoked. The extent of airflow obstruction was similarly associated with left ventricular structure and function, and smoking status had similar modifying effects on these associations. Percent emphysema and airflow obstruction were not associated with the left ventricular ejection fraction.ConclusionsIn a population-based study, a greater extent of emphysema on CT scanning and more severe airflow obstruction were linearly related to impaired left ventricular filling, reduced stroke volume, and lower cardiac output without changes in the ejection fraction.
| S-EPMC2887729 | biostudies-literature