Goodness of Fit for the Geometric Distribution

A Neyman-type smooth test of goodness of fit is derived for the geometric distribution. Some small-sample critical points are given, with two examples.     

A Comparison Between Several Goodness of Fit Tests for Cox's Model

A comparison is made between two approaches to testing goodness of fit of Cox's regression model for survival data. The first approach is based on the inclusion of time dependent covariates, whereas the second one is based on the autocovariance of successive contributions to the derivative of the loglikelihood. It appears that the second test is most appropriate for testing in situations where the structure of the departure from proportional hazards is not known a priori. An approximate expression for the relative efficiency of the two test procedures is presented.     

S-Sample Smooth Goodness of Fit Testing: Rederivation and Monte Carlo Assessment

S-sample smooth goodness of fit tests may be constructed using components from one sample goodness of fit testing. Each sample could be assessed for consistency with a target distribution using these components, although that is not our objective here. Contrasts in the components may be used to assess consistency of the samples with each other. If all the samples are consistent, we could then conveniently perform a one-sample goodness of fit test for the target distribution. If the samples are not consistent, an LSD-type analysis can be performed on the one-sample components to identify where the differences between occur. This approach gives a detailed and informative scrutiny of the data.     

Simulation of Clinical Diagnosis: A Comparative Study

This paper presents a comparison between three different modes of simulation of the diagnostic process—a computer-based system, a verbal mode, and a further mode in which cards were selected from a large board. A total of 34 subjects worked through a series of 444 diagnostic simulations.The verbal mode was found to be most enjoyable and realistic. At the board, considerable amounts of extra irrelevant data were selected. At the computer, the users asked the same questions every time, whether or not they were relevant to the particular diagnosis. They also found the teletype distracting, noisy, and slow.The need for an acceptable simulation system remains, and at present our Minisim and verbal modes are proving useful in training junior clinical students. Future simulators should be flexible, economical, and acceptably realistic—and to us this latter criterion implies the two-way use of speech. We are currently developing and testing such a system.     

Goodness of Fit of Discriminant Functions from the Vector Space of Fixed Variates

Alternative proofs of some of KSHIRSAGAR's (1971) results on testing discriminant functions or canonical variables in the vector space of fixed variates are given. These results are derived in terms of the original variates unlike KSHIRSAGAR (1971) who derives the results by using random orthogonal transformations and triangular decompositions of the original matrix variates.     

The Dilemma of Heterogeneity Tests in Meta-Analysis: A Challenge from a Simulation Study

IntroductionAfter several decades’ development, meta-analysis has become the pillar of evidence-based medicine. However, heterogeneity is still the threat to the validity and quality of such studies. Currently, Q and its descendant I² (I square) tests are widely used as the tools for heterogeneity evaluation. The core mission of this kind of test is to identify data sets from similar populations and exclude those are from different populations. Although Q and I² are used as the default tool for heterogeneity testing, the work we present here demonstrates that the robustness of these two tools is questionable.ConclusionsEvery day, meta-analysis studies which contain flawed data analysis are emerging and passed on to clinical practitioners as “updated evidence”. Using this kind of evidence that contain heterogeneous data sets leads to wrong conclusion, makes chaos in clinical practice and weakens the foundation of evidence-based medicine. We suggest more strict applications of meta-analysis: it should only be applied to those synthesized trials with small sample sizes. We call upon that the tools of evidence-based medicine should keep up-to-dated with the cutting-edge technologies in data science. Clinical research data should be made available publicly when there is any relevant article published so the research community could conduct in-depth data mining, which is a better alternative for meta-analysis in many instances.     

A Comparative Study and a Phylogenetic Exploration of the Compositional Architectures of Mammalian Nuclear Genomes

For the past four decades the compositional organization of the mammalian genome posed a formidable challenge to molecular evolutionists attempting to explain it from an evolutionary perspective. Unfortunately, most of the explanations adhered to the “isochore theory,” which has long been rebutted. Recently, an alternative compositional domain model was proposed depicting the human and cow genomes as composed mostly of short compositionally homogeneous and nonhomogeneous domains and a few long ones. We test the validity of this model through a rigorous sequence-based analysis of eleven completely sequenced mammalian and avian genomes. Seven attributes of compositional domains are used in the analyses: (1) the number of compositional domains, (2) compositional domain-length distribution, (3) density of compositional domains, (4) genome coverage by the different domain types, (5) degree of fit to a power-law distribution, (6) compositional domain GC content, and (7) the joint distribution of GC content and length of the different domain types. We discuss the evolution of these attributes in light of two competing phylogenetic hypotheses that differ from each other in the validity of clade Euarchontoglires. If valid, the murid genome compositional organization would be a derived state and exhibit a high similarity to that of other mammals. If invalid, the murid genome compositional organization would be closer to an ancestral state. We demonstrate that the compositional organization of the murid genome differs from those of primates and laurasiatherians, a phenomenon previously termed the “murid shift,” and in many ways resembles the genome of opossum. We find no support to the “isochore theory.” Instead, our findings depict the mammalian genome as a tapestry of mostly short homogeneous and nonhomogeneous domains and few long ones thus providing strong evidence in favor of the compositional domain model and seem to invalidate clade Euarchontoglires.     

Using the Past to Predict the Present: Confidence Intervals for Regression Equations in Phylogenetic Comparative Methods

Two phylogenetic comparative methods, independent contrasts and generalized least squares models, can be used to determine the statistical relationship between two or more traits. We show that the two approaches are functionally identical and that either can be used to make statistical inferences about values at internal nodes of a phylogenetic tree (hypothetical ancestors), to estimate relationships between characters, and to predict values for unmeasured species. Regression equations derived from independent contrasts can be placed back onto the original data space, including computation of both confidence intervals and prediction intervals for new observations. Predictions for unmeasured species (including extinct forms) can be made increasingly accurate and precise as the specificity of their placement on a phylogenetic tree increases, which can greatly increase statistical power to detect, for example, deviation of a single species from an allometric prediction. We reexamine published data for basal metabolic rates (BMR) of birds and show that conventional and phylogenetic allometric equations differ significantly. In new results, we show that, as compared with nonpasserines, passerines exhibit a lower rate of evolution in both body mass and mass-corrected BMR; passerines also have significantly smaller body masses than their sister clade. These differences may justify separate, clade-specific allometric equations for prediction of avian basal metabolic rates.     

Assessing the Effects of Climate on Host-Parasite Interactions: A Comparative Study of European Birds and Their Parasites

Background

Climate change potentially has important effects on distribution, abundance, transmission and virulence of parasites in wild populations of animals.

Methodology/Principal Finding

Here we analyzed paired information on 89 parasite populations for 24 species of bird hosts some years ago and again in 2010 with an average interval of 10 years. The parasite taxa included protozoa, feather parasites, diptera, ticks, mites and fleas. We investigated whether change in abundance and prevalence of parasites was related to change in body condition, reproduction and population size of hosts. We conducted analyses based on the entire dataset, but also on a restricted dataset with intervals between study years being 5–15 years. Parasite abundance increased over time when restricting the analyses to datasets with an interval of 5–15 years, with no significant effect of changes in temperature at the time of breeding among study sites. Changes in host body condition and clutch size were related to change in temperature between first and second study year. In addition, changes in clutch size, brood size and body condition of hosts were correlated with change in abundance of parasites. Finally, changes in population size of hosts were not significantly related to changes in abundance of parasites or their prevalence.

Conclusions/Significance

Climate change is associated with a general increase in parasite abundance. Variation in laying date depended on locality and was associated with latitude while body condition of hosts was associated with a change in temperature. Because clutch size, brood size and body condition were associated with change in parasitism, these results suggest that parasites, perhaps mediated through the indirect effects of temperature, may affect fecundity and condition of their hosts. The conclusions were particularly in accordance with predictions when the restricted dataset with intervals of 5–15 years was used, suggesting that short intervals may bias findings.     

Comparative Efficacy and Acceptability of Antidepressants in Parkinson's Disease: A Network Meta-Analysis

Background

Depression is a common non-motor symptom in patients with Parkinson''s disease (PD). There are many kinds of antidepressants being used, such as tricyclic antidepressants (TCAs), selective serotonin reuptake inhibitors (SSRIs), serotonin and norepinephrine reuptake inhibitors (SNRIs), and Dopamine agonists which are suggested as alternative antidepressants for the treatment of depression in PD. Which one should we choose first? Literatures have shown inconsistent results.

Methods

We conducted a network meta-analysis of randomized controlled trials to compare the efficacy and acceptability of therapeutic methods for the treatment of depression in Parkinson''s disease.

Results

We used the odds ratios (OR) as effect size firstly and the results indicated no statistical significance between each compared intervention. Then we used the logarithm of the individual odds ratios as effect size. With efficacy of TCAs as the standard of comparison, the degree of incoherence (a measure of how closely the entire network fits together) was small (ω =  4.824827e-05). The logor were: SSRIs −0.69 (95% CI −1.28– −0.10); Pramipexole −0.73 (−1.71– −0.26); Pergolide −1.97 (−3.67– 0.27); SNRIs −0.86 (−1.86– 0.15); Placebo −1.24 (−1.99– −0.50). With Placebo as the standard of comparison, the logor were: TCAs 1.24 (0.50– 1.99); SSRIs 0.55 (−0.03– 1.13); Pramipexole 0.51 (−0.12– 1.15); Pergolide −0.73 (−2.25– 0.80); SNRIs 0.38 (−0.42– 1.19); TCAs, pramipexole, pergolide and SNRIs showed better profile of acceptability, leading to significant fewer discontinuations than that of SSRIs.

Conclusions

There is insufficient evidence to support antidepressant efficacy for SSRIs, pramipexole, pergolide and SNRIs. TCAs might be the best choice when starting antidepressant treatment in patients of Parkinson''s disease because it has the most favorable balance between benefits and acceptability, followed by pramipexole and SNRIs, SSRIs might be the last choice.     

Comparative Efficacy of Lamivudine and Emtricitabine: A Systematic Review and Meta-Analysis of Randomized Trials

Introduction

Lamivudine and emtricitabine are considered equivalent by several guidelines, but evidence of comparable efficacy is conflicting.

Methods

We searched two databases up to June 30 2013 to identify randomized and quasi-randomized trials in which lamivudine and emtricitabine were used as part of combination antiretroviral therapy for treatment-naïve or experienced HIV-positive adult patients. We only included trials where partner drugs in the regimen were identical or could be considered to be comparable. We allowed for comparisons between tenofovir and abacavir provided the study population did not begin treatment with a viral load >100,000 copies/ml.

Results

12 trials contributed 15 different randomized comparisons providing data on 2251 patients receiving lamivudine and 2662 patients receiving emtricitabine. Treatment success was not significantly different in any of the 12 trials. In the three trials that directly compared lamivudine and emtricitabine, the relative risk for achieving treatment success was non-significant (RR 1.03 95%CI 0.96-1.10). For all trials combined, the pooled relative risk for treatment success was not significantly different (RR 1.00, 95%CI 0.97–1.02). No heterogeneity was observed (I ² = 0). Similarly, there was no difference in the pooled relative risk for treatment failure (RR 1.08, 95%CI 0.94–1.22, I ² = 3.4%).

Conclusions

The findings of this systematic review suggest that lamivudine and emtricitabine are clinically equivalent.     

Assessing the Quality of Care for Pneumonia in Integrated Community Case Management: A Cross-Sectional Mixed Methods Study

Background

Pneumonia is the leading infectious cause of mortality in children under five worldwide. Community-level interventions, such as integrated community case management, have great potential to reduce the burden of pneumonia, as well as other diseases, especially in remote populations. However, there are still questions as to whether community health workers (CHW) are able to accurately assess symptoms of pneumonia and prescribe appropriate treatment. This research addresses limitations of previous studies using innovative methodology to assess the accuracy of respiratory rate measurement by CHWs and provides new evidence on the quality of care given for children with symptoms of pneumonia. It is one of few that assesses CHW performance in their usual setting, with independent re-examination by experts, following a considerable period of time post-training of CHWs.

Methods

In this cross-sectional mixed methods study, 1,497 CHW consultations, conducted by 90 CHWs in two districts of Luapula province, Zambia, were directly observed, with measurement of respiratory rate for children with suspected pneumonia recorded by video. Using the video footage, a retrospective reference standard assessment of respiratory rate was conducted by experts. Counts taken by CHWs were compared against the reference standard and appropriateness of the treatment prescribed by CHWs was assessed. To supplement observational findings, three focus group discussions and nine in depth interviews with CHWs were conducted.

Results and Conclusion

The findings support existing literature that CHWs are capable of measuring respiratory rates and providing appropriate treatment, with 81% and 78% agreement, respectively, between CHWs and experts. Accuracy in diagnosis could be strengthened through further training and the development of improved diagnostic tools appropriate for resource-poor settings.     

A Survey of Methods for Constructing Rooted Phylogenetic Networks

Rooted phylogenetic networks are primarily used to represent conflicting evolutionary information and describe the reticulate evolutionary events in phylogeny. So far a lot of methods have been presented for constructing rooted phylogenetic networks, of which the methods based on the decomposition property of networks and by means of the incompatible graph (such as the CASS, the LNETWORK and the BIMLR) are more efficient than other available methods. The paper will discuss and compare these methods by both the practical and artificial datasets, in the aspect of the running time of the methods and the effective of constructed phylogenetic networks. The results show that the LNETWORK can construct much simper networks than the others.     

2种核酸染色方法的比较

目的:比较前染和后染等2种核酸染色方法对凝胶中DNA的染色效果,及其对染料染色灵敏度的影响,并验证新型核酸染色剂SYBRGreenⅠ能否代替传统染料溴化乙锭(EB)用于常规电泳中DNA的染色。方法:分别用SYBRGreenⅠ与EB采用2种不同的方法对凝胶中的DNA进行染色。结果:前染和后染的染色效果无显著差别,2种染料都能显示出10ng以下的DNA条带。结论:前染和后染方法的染色效果相当,染料SYBRGreenⅠ和EB均可用于这2种染色方法;新型染料SYBRGreenⅠ可代替强致癌性染料EB,用于常规凝胶中DNA的染色。     

A Comparative Study of Two Ambulatory Core Temperature Assessment Methods

Background. Given the need to identify reliable non-invasive solutions for core temperature ambulatory monitoring, the purpose of this study was to evaluate the performance of zero-heat-flux (ZHF) temperature sensor on the forehead ($T_{\mathrm{COzhf}}$) by comparing it with intestinal temperature ($T_{\mathrm{COpill}}$) in different ambient and physiological conditions.Methods. Seven trained male subjects were followed during a 45-min rest period (STA) and a 25-min self-regulated cycling exercise performed in neutral (TMP, 22.8?°C) and hot (HOT, 38.5 °C) ambient temperature.Results.$T_{\mathrm{COzhf}}$ values differed from $T_{\mathrm{COpill}}$ of ?0.23 ± 0.13 in STA, 0.15 ± 0.30 °C in TMP and $0.28\pm 0.38$?°C in HOT. The 95% limits of agreement showed an acceptable bias between $T_{\mathrm{COzhf}}$ and $T_{\mathrm{COpill}}$ in STA (±0.26?°C), but not in TMP and HOT (±0.60 and ±0.75?°C).Conclusion. The non-invasive ZHF sensor gave an accurate estimation of $T_{\mathrm{COpill}}$ in steady state but not during exercise. However, complementary results let suppose that ZHF performance is not affected by ambient conditions and could be a relevant alternative for deep body temperature measurement during whole-body heat stress.