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1.
Background
Zipf''s law and Heaps'' law are two representatives of the scaling concepts, which play a significant role in the study of complexity science. The coexistence of the Zipf''s law and the Heaps'' law motivates different understandings on the dependence between these two scalings, which has still hardly been clarified.Methodology/Principal Findings
In this article, we observe an evolution process of the scalings: the Zipf''s law and the Heaps'' law are naturally shaped to coexist at the initial time, while the crossover comes with the emergence of their inconsistency at the larger time before reaching a stable state, where the Heaps'' law still exists with the disappearance of strict Zipf''s law. Such findings are illustrated with a scenario of large-scale spatial epidemic spreading, and the empirical results of pandemic disease support a universal analysis of the relation between the two laws regardless of the biological details of disease. Employing the United States domestic air transportation and demographic data to construct a metapopulation model for simulating the pandemic spread at the U.S. country level, we uncover that the broad heterogeneity of the infrastructure plays a key role in the evolution of scaling emergence.Conclusions/Significance
The analyses of large-scale spatial epidemic spreading help understand the temporal evolution of scalings, indicating the coexistence of the Zipf''s law and the Heaps'' law depends on the collective dynamics of epidemic processes, and the heterogeneity of epidemic spread indicates the significance of performing targeted containment strategies at the early time of a pandemic disease. 相似文献2.
Background
Zipf''s discovery that word frequency distributions obey a power law established parallels between biological and physical processes, and language, laying the groundwork for a complex systems perspective on human communication. More recent research has also identified scaling regularities in the dynamics underlying the successive occurrences of events, suggesting the possibility of similar findings for language as well.Methodology/Principal Findings
By considering frequent words in USENET discussion groups and in disparate databases where the language has different levels of formality, here we show that the distributions of distances between successive occurrences of the same word display bursty deviations from a Poisson process and are well characterized by a stretched exponential (Weibull) scaling. The extent of this deviation depends strongly on semantic type – a measure of the logicality of each word – and less strongly on frequency. We develop a generative model of this behavior that fully determines the dynamics of word usage.Conclusions/Significance
Recurrence patterns of words are well described by a stretched exponential distribution of recurrence times, an empirical scaling that cannot be anticipated from Zipf''s law. Because the use of words provides a uniquely precise and powerful lens on human thought and activity, our findings also have implications for other overt manifestations of collective human dynamics. 相似文献3.
Background
Zipf''s law states that the relationship between the frequency of a word in a text and its rank (the most frequent word has rank , the 2nd most frequent word has rank ,…) is approximately linear when plotted on a double logarithmic scale. It has been argued that the law is not a relevant or useful property of language because simple random texts - constructed by concatenating random characters including blanks behaving as word delimiters - exhibit a Zipf''s law-like word rank distribution.Methodology/Principal Findings
In this article, we examine the flaws of such putative good fits of random texts. We demonstrate - by means of three different statistical tests - that ranks derived from random texts and ranks derived from real texts are statistically inconsistent with the parameters employed to argue for such a good fit, even when the parameters are inferred from the target real text. Our findings are valid for both the simplest random texts composed of equally likely characters as well as more elaborate and realistic versions where character probabilities are borrowed from a real text.Conclusions/Significance
The good fit of random texts to real Zipf''s law-like rank distributions has not yet been established. Therefore, we suggest that Zipf''s law might in fact be a fundamental law in natural languages. 相似文献4.
It is well-known that word frequencies arrange themselves according to Zipf''s law. However, little is known about the dependency of the parameters of the law and the complexity of a communication system. Many models of the evolution of language assume that the exponent of the law remains constant as the complexity of a communication systems increases. Using longitudinal studies of child language, we analysed the word rank distribution for the speech of children and adults participating in conversations. The adults typically included family members (e.g., parents) or the investigators conducting the research. Our analysis of the evolution of Zipf''s law yields two main unexpected results. First, in children the exponent of the law tends to decrease over time while this tendency is weaker in adults, thus suggesting this is not a mere mirror effect of adult speech. Second, although the exponent of the law is more stable in adults, their exponents fall below 1 which is the typical value of the exponent assumed in both children and adults. Our analysis also shows a tendency of the mean length of utterances (MLU), a simple estimate of syntactic complexity, to increase as the exponent decreases. The parallel evolution of the exponent and a simple indicator of syntactic complexity (MLU) supports the hypothesis that the exponent of Zipf''s law and linguistic complexity are inter-related. The assumption that Zipf''s law for word ranks is a power-law with a constant exponent of one in both adults and children needs to be revised. 相似文献
5.
Markus Fabrizii Farid Moinfar Herbert F. Jelinek Audrey Karperien Helmut Ahammer 《PloS one》2014,9(10)
Introduction
Cervical intraepithelial neoplasias (CIN) represent precursor lesions of cervical cancer. These neoplastic lesions are traditionally subdivided into three categories CIN 1, CIN 2, and CIN 3, using microscopical criteria. The relation between grades of cervical intraepithelial neoplasia (CIN) and its fractal dimension was investigated to establish a basis for an objective diagnosis using the method proposed.Methods
Classical evaluation of the tissue samples was performed by an experienced gynecologic pathologist. Tissue samples were scanned and saved as digital images using Aperio scanner and software. After image segmentation the box counting method as well as multifractal methods were applied to determine the relation between fractal dimension and grades of CIN. A total of 46 images were used to compare the pathologist''s neoplasia grades with the predicted groups obtained by fractal methods.Results
Significant or highly significant differences between all grades of CIN could be found. The confusion matrix, comparing between pathologist''s grading and predicted group by fractal methods showed a match of 87.1%. Multifractal spectra were able to differentiate between normal epithelium and low grade as well as high grade neoplasia.Conclusion
Fractal dimension can be considered to be an objective parameter to grade cervical intraepithelial neoplasia. 相似文献6.
Background
Here we continue our efforts to use methods developed in the folding mechanism community to both better understand and improve structure prediction. Our previous work demonstrated that Rosetta''s coarse-grained potentials may actually impede accurate structure prediction at full-atom resolution. Based on this work we postulated that it may be time to work completely at full-atom resolution but that doing so may require more careful attention to the kinetics of convergence.Methodology/Principal Findings
To explore the possibility of working entirely at full-atom resolution, we apply enhanced sampling algorithms and the free energy theory developed in the folding mechanism community to full-atom protein structure prediction with the prominent Rosetta package. We find that Rosetta''s full-atom scoring function is indeed able to recognize diverse protein native states and that there is a strong correlation between score and Cα RMSD to the native state. However, we also show that there is a huge entropic barrier to folding under this potential and the kinetics of folding are extremely slow. We then exploit this new understanding to suggest ways to improve structure prediction.Conclusions/Significance
Based on this work we hypothesize that structure prediction may be improved by taking a more physical approach, i.e. considering the nature of the model thermodynamics and kinetics which result from structure prediction simulations. 相似文献7.
Background
Canada''s Neo Rhino Party, a joke political party created in 2006 as a successor to the Parti Rhinocéros, is planning a new regulation to repeal the law of gravity, which could have an important impact on diseases attributable to gravity on earth.Methods
We sought to estimate the number of quality-adjusted life-years that would be saved if the proposed regulation is passed and determine the cost-effectiveness of adapting Boris Volfson''s antigravity machine1 for use on earth. We performed an economic analysis using a hidden Markov model.Results
Our results suggest that a microgravity environment would save over 2 million quality-adjusted life-years. The cost for every quality-adjusted life-year saved is estimated to be $328.Interpretation
Microgravity is the solution to the health care crisis in Canada. In addition, using technological, statistical and medical jargon gives us the opportunity to defy the laws of physics, mathematics and medicine.Canada''s Neo Rhino Party is a joke federal political party that was created in Montréal, Quebec, in 2006 as the successor to the Parti Rhinocéros. Commonly called the Rhinoceros Party in English, this party was a registered political party in Canada from the 1960s to the 1990s. It was founded in 1963 by Jacques Ferron, a Canadian physician and author. The party''s basic credo was “a promise to keep none of our promises.” Its election platforms comprised impossible schemes that were designed to amuse and entertain the voting public. Some Rhinoceros Party promises included reducing the speed of light because it''s much too fast, paving Manitoba to create the world''s largest parking lot, providing higher education by building taller schools and repealing the law of gravity. When this last promise was made in the 1980s, it was unthinkable, that is, until Boris Volfson of Huntington, Indiana, received US Patent 6 960 975 for his design of an antigravity machine.1 The Neo Rhino Party is currently planning a new regulation to repeal the law of gravity that could have an important impact on diseases and other health outcomes attributable to gravity on earth. 相似文献8.
9.
Objective
At present, only the number of metastatic lymph nodes (LNs+) is used for the pN category of AJCC TNM system for colon cancer. Recently, the ratio of metastatic to examined lymph nodes (LNR) has been reported to represent powerful independent predictive capacity in colon cancer. We sought to propose a novel category (nLN) which intergrades LNR and LNs+ into the AJCC staging system for colon cancer.Design
34476 patients from the National Cancer Institute''s Surveillance, Epidemiology, and End Results (SEER) dataset with stage III colon cancer were reviewed. Harrell''s C statistic was used to evaluate the predictive capacity. The Cox proportional hazards model was used to construct a novel category.Results
The LNR category had more predictive capacity than the pN category in whole groups of patients (Harrell''s C index: 0.6194 vs 0.6113, p = 0.003). Subgroup analysis showed that the LNR category was not better than pN category in predictive capacity if the number of lymph nodes examined was more than 13. We also found that there was significant survival heterogeneity among different pN categories at the same LNR category (P<0.001). The Harrell''s C index for our nLN category which intergrades LNR and LNs+ was 0.6228, which was significant higher than that of the pN category (Harrell''s C index: 0.6113, P<0.001) or LNR category (Harrell''s C index: 0.6194, P = 0.005), respectively.Conclusion
To evaluate the prognosis of colon cancer, our nLN category which intergrades LNR with LNs+ is more accurate than the pN category or LNR category, respectively. 相似文献10.
Bilitchenko L Liu A Cheung S Weeding E Xia B Leguia M Anderson JC Densmore D 《PloS one》2011,6(4):e18882
Background
Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts.Results
We illustrate Eugene''s capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene''s ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively.Conclusions
Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly. 相似文献11.
Context
Prior research has faulted the US News and World Report hospital specialty rankings for excessive reliance on reputation, a subjective measure of a hospital''s performance.Objective
To determine whether and to what extent reputation correlates with objective measures of research productivity among cancer hospitals.Design
A retrospective observational study.Setting
Automated search of NIH Reporter, BioEntrez, BioMedline and Clinicaltrials.gov databases.Participants
The 50 highest ranked cancer hospitals in 2013''s US News and World Report Rankings.Exposure
We ascertained the number of NCI funded grants, and the cumulative funds received by each cancer center. Additionally, we identified the number of phase I, phase II, and phase III studies published and indexed in MEDLINE, and registered at clinicaltrials.gov. All counts were over the preceding 5 years. For published articles, we summed the impact factor of the journals in which they appeared. Trials were attributed to centers on the basis of the affiliation of the lead author or study principal investigator.Main Outcome
Correlation coefficients from simple and multiple linear regressions for measures of research productivity and a center''s reputation.Results
All measures of research productivity demonstrated robust correlation with reputation (mean r-squared = 0.65, median r-squared = 0.68, minimum r-squared = .41, maximum r-squared = 0.80). A multivariable model showed that 93% of the variation in reputation is explained by objective measures.Conclusion
Contrary to prior criticism, the majority of reputation, used in US News and World Rankings, can be explained by objective measures of research productivity among cancer hospitals. 相似文献12.
Cheptou PO 《Annals of botany》2012,109(3):633-641
Background
Baker''s Law states that colonization by self-compatible organisms is more likely to be successful than colonization by self-incompatible organisms because of the ability for self-compatible organisms to produce offspring without pollination agents. This simple model has proved very successful in plant ecology and has been applied to various contexts, including colonizing or ruderal species, islands colonizers, invasive species or mating system variation across distribution ranges. Moreover, it is one of the only models in population biology linking two traits of major importance in ecology, namely dispersal and mating system. Although Baker''s Law has stimulated a large number of empirical studies reporting the association of self-fertilization and colonizing ability in various contexts, the data have not established a general pattern for the association of traits.Scope
In this paper, a critical position is adopted to discuss and clarify Baker''s Law. From the literature referring to Baker''s Law, an analysis made regarding how mating success is considered in such studies and discrepancies with population genetics theory of mating systems are highlighted. The data reporting the association of self-fertilization and colonizing ability are also briefly reviewed and the potential bias in interpretation is discussed. Lastly, a recent theoretical model analysing the link between colonizing ability and self-fertilization is considered.Conclusions
Evolutionary predictions are actually more complex than Baker''s intuitive arguments. It appears that Baker''s Law encompasses a variety of ecological scenarios, which cannot be considered a priori as equivalent. Questioning what has been considered as self-evident for more than 50 years seems a reasonable objective to analyse in-depth dispersal and mating system traits. 相似文献13.
Sei J. Lee Christine S. Ritchie Kristine Yaffe Irena Stijacic Cenzer Deborah E. Barnes 《PloS one》2014,9(12)
Background
Mild cognitive impairment is often a precursor to dementia due to Alzheimer''s disease, but many patients with mild cognitive impairment never develop dementia. New diagnostic criteria may lead to more patients receiving a diagnosis of mild cognitive impairment.Objective
To develop a prediction index for the 3-year risk of progression from mild cognitive impairment to dementia relying only on information that can be readily obtained in most clinical settings.Design and Participants
382 participants diagnosed with amnestic mild cognitive impairment enrolled in the Alzheimer''s Disease Neuroimaging Initiative (ADNI), a multi-site, longitudinal, observational study.Main Predictors Measures
Demographics, comorbid conditions, caregiver report of participant symptoms and function, and participant performance on individual items from basic neuropsychological scales.Main Outcome Measure
Progression to probable Alzheimer''s disease.Key Results
Subjects had a mean (SD) age of 75 (7) years and 43% progressed to probable Alzheimer''s disease within 3 years. Important independent predictors of progression included being female, resisting help, becoming upset when separated from caregiver, difficulty shopping alone, forgetting appointments, number of words recalled from a 10-word list, orientation and difficulty drawing a clock. The final point score could range from 0 to 16 (mean [SD]: 4.2 [2.9]). The optimism-corrected Harrell''s c-statistic was 0.71(95% CI: 0.68–0.75). Fourteen percent of subjects with low risk scores (0–2 points, n = 124) converted to probable Alzheimer''s disease over 3 years, compared to 51% of those with moderate risk scores (3–8 points, n = 223) and 91% of those with high risk scores (9–16 points, n = 35).Conclusions
An index using factors that can be obtained in most clinical settings can predict progression from amnestic mild cognitive impairment to probable Alzheimer''s disease and may help clinicians differentiate between mild cognitive impairment patients at low vs. high risk of progression. 相似文献14.
Ariane Ghekiere Jelle Van Cauwenberg Bas de Geus Peter Clarys Greet Cardon Jo Salmon Ilse De Bourdeaudhuij Benedicte Deforche 《PloS one》2014,9(9)
Background
Environmental factors are found to influence transport-related physical activity, but have rarely been studied in relation with cycling for transport to various destinations in 10–12 yr old children. The current qualitative study used ‘bike-along interviews’ with children and parents to allow discussion of detailed environmental factors that may influence children''s cycling for transport, while cycling in the participant''s neighborhood.Methods
Purposeful convenience sampling was used to recruit 35 children and one of their parents residing in (semi-) urban areas. Bike-along interviews were conducted to and from a randomly chosen destination (e.g. library) within a 15 minutes'' cycle trip in the participant''s neighborhood. Participants wore a GoPro camera to objectively assess environmental elements, which were subsequently discussed with participants. Content analysis and arising themes were derived using a grounded theory approach.Results
The discussed environmental factors were categorized under traffic, urban design, cycling facilities, road design, facilities at destination, aesthetics, topography, weather, social control, stranger danger and familiar environment. Across these categories many environmental factors were (in)directly linked to road safety. This was illustrated by detailed discussions of the children''s visibility, familiarity with specific traffic situations, and degree of separation, width and legibility of cycle facilities.Conclusion
Road safety is of major concern in this 10–12 yr old study population. Bike-along interviews were able to identify new, detailed and context-specific physical environmental factors which could inform policy makers to promote children''s cycling for transport. However, future studies should investigate whether hypothetical changes to such micro environmental features influence perceptions of safety and if this in turn could lead to changes in children''s cycling for transport. 相似文献15.
Purpose
In the developed countries, the incidence of esophageal adenocarcinoma (EAC) is increasing over recent decades. The purpose of this meta-analysis was to arrive at quantitative conclusions about the contribution of alcohol intakes and the progression of Barrett''s esophagus.Methods
A comprehensive, systematic bibliographic search of medical literature published up to Oct 2013 was conducted to identify relevant studies. A meta-analysis was conducted for alcohol consumption on the Barrett''s esophagus progression.Results
A total of 882 cases in 6,867 individuals from 14 observational studies were indemnified in this meta-analysis. The result of this current meta-analysis, including 10 case-control and 4 cohort studies, indicated that alcohol consumption was not associated with the neoplastic progression in Barrett''s esophagus (RR, 1.17; 95% CI, 0.93–1.48). When stratified by the study designs, no significant association was detected in either high vs low group or ever vs never group.Conclusions
Alcohol drinking is not associated with risk of neoplastic progression in Barrett''s esophagus. Further well designed studies are needed in this area. 相似文献16.
Aline De Vleminck Koen Pardon Kim Beernaert Reginald Deschepper Dirk Houttekier Chantal Van Audenhove Luc Deliens Robert Vander Stichele 《PloS one》2014,9(1)
Background
The long-term and often lifelong relationship of general practitioners (GPs) with their patients is considered to make them the ideal initiators of advance care planning (ACP). However, in general the incidence of ACP discussions is low and ACP seems to occur more often for cancer patients than for those with dementia or heart failure.Objective
To identify the barriers, from GPs'' perspective, to initiating ACP and to gain insight into any differences in barriers between the trajectories of patients with cancer, heart failure and dementia.Method
Five focus groups were held with GPs (n = 36) in Flanders, Belgium. The focus group discussions were transcribed verbatim and analyzed using the method of constant comparative analysis.Results
Three types of barriers were distinguished: barriers relating to the GP, to the patient and family and to the health care system. In cancer patients, a GP''s lack of knowledge about treatment options and the lack of structural collaboration between the GP and specialist were expressed as barriers. Barriers that occured more often with heart failure and dementia were the lack of GP familiarity with the terminal phase, the lack of key moments to initiate ACP, the patient''s lack of awareness of their diagnosis and prognosis and the fact that patients did not often initiate such discussions themselves. The future lack of decision-making capacity of dementia patients was reported by the GPs as a specific barrier for the initiation of ACP.Conclusion
The results of our study contribute to a better understanding of the factors hindering GPs in initiating ACP. Multiple barriers need to be overcome, of which many can be addressed through the development of practical guidelines and educational interventions. 相似文献17.
Objectives
The purpose of this study was to examine the change in health status of China''s adult population between the years of 2003 and 2008 due to rapid economic growth and medical system improvement.Methods
Data from the third and fourth Chinese national health services surveys covering 141,927 residents in 2003 and 136,371 residents in 2008 who were aged >18 years were analyzed.Results
Chinese respondents in 2008 were more likely to report disease than in 2003. Smoking slightly decreased among men and women, and regular exercise showed much improvement. Stratified analyses revealed significant subpopulation disparities in rate ratios for 2008/2003 in the presence of chronic disease, with greater increases among women, elderly, the Han nationality, unmarried and widow, illiterate, rural, and regions east of China than other groups.Conclusions
Chinese adults in 2008 had worse health status than in 2003 in terms of presence of chronic disease. China''s reform of health care will face more complex challenges in coming years from the deteriorating health status in Chinese adults. 相似文献18.
Aim
The analysis of barriers responsible for low recruitment of older patients in clinical trials and presentation of possible solutions are the subject of this review.Background
Europe''s population is ageing, and the group of people who more frequently develop neoplasms increases. Oncologists are confronted with a new challenge – how to treat cancer in this group of patients, especially considering the lack of Evidence Based Medicine (EBM) guidelines for treatment of cancer in the elderly population.Materials and methods
Medline search and analysis of studies published between 1999 and 2012, containing key words: senior adults, cancer, elderly in clinical trials.Results
Detailed analysis of relevant studies demonstrated that senior adults are underrepresented in clinical trials. Moreover, there is a lack of trials exclusively designed for this heterogeneous group of patients. The analysis of reasons for low recruitment of older patients in clinical trials revealed barriers dependent on patient''s and physician''s attitudes as well as institutional and logistic problems.Conclusions
It is necessary to widen the scale of trials of all phases in the group of seniors with appropriate assessment of toxicity. This will allow a proper stratification and obtaining representative groups for statistical analysis and credible trial results. Another priority is the design of trials dedicated exclusively to the elderly. 相似文献19.
Background
Understanding the distribution of marine biodiversity is a crucial first step towards the effective and sustainable management of marine ecosystems. Recent efforts to collate location records from marine surveys enable us to assemble a global picture of recorded marine biodiversity. They also effectively highlight gaps in our knowledge of particular marine regions. In particular, the deep pelagic ocean – the largest biome on Earth – is chronically under-represented in global databases of marine biodiversity.Methodology/Principal Findings
We use data from the Ocean Biogeographic Information System to plot the position in the water column of ca 7 million records of marine species occurrences. Records from relatively shallow waters dominate this global picture of recorded marine biodiversity. In addition, standardising the number of records from regions of the ocean differing in depth reveals that regardless of ocean depth, most records come either from surface waters or the sea bed. Midwater biodiversity is drastically under-represented.Conclusions/Significance
The deep pelagic ocean is the largest habitat by volume on Earth, yet it remains biodiversity''s big wet secret, as it is hugely under-represented in global databases of marine biological records. Given both its value in the provision of a range of ecosystem services, and its vulnerability to threats including overfishing and climate change, there is a pressing need to increase our knowledge of Earth''s largest ecosystem. 相似文献20.
Sabina Gainotti Susanna Fusari Imperatori Stefania Spila-Alegiani Laura Maggiore Francesca Galeotti Nicola Vanacore Carlo Petrini Roberto Raschetti Claudio Mariani Francesca Clerici 《PloS one》2010,5(6)