Generalized linear mixed models(GLMMs)have been widely used in contemporary ecology studies.However,determination of the relative importance of collinear predictors(i.e.fixed effects)to response variables is one of th...Generalized linear mixed models(GLMMs)have been widely used in contemporary ecology studies.However,determination of the relative importance of collinear predictors(i.e.fixed effects)to response variables is one of the challenges in GLMMs.Here,we developed a novel R package,glmm.hp,to decompose marginal R2^(2)explained by fixed effects in GLMMs.The algorithm of glmm.hp is based on the recently proposed approach‘average shared variance’i.e.used for multivariate analysis.We explained the principle and demonstrated the use of this package by simulated dataset.The output of glmm.hp shows individual marginal R2^(2)s that can be used to evaluate the relative importance of predictors,which sums up to the overall marginal R2^(2).Overall,we believe the glmm.hp package will be helpful in the interpretation of GLMM outcomes.展开更多
Background: Most patients infected with Helicobacter pylori show no clinical symptoms. Nonetheless, approximately 10% to 20% of these patients will develop peptic ulcers and 1% will develop gastric cancer. The Interna...Background: Most patients infected with Helicobacter pylori show no clinical symptoms. Nonetheless, approximately 10% to 20% of these patients will develop peptic ulcers and 1% will develop gastric cancer. The International Agency for Cancer Research has classified Helicobacter pylori as a Group 1 carcinogen. Materials and Methods: Drinking water samples from 20 cantons situated in areas of low and high incidence of gastric cancer in Costa Rica were analyzed. Water samples were concentrated and the nitrocellulose filter was cultivated for later molecular identification of Helicobacter pylori using the glmM marker. The tumor necrosis factor-alpha inducing protein (Tipalpha TNF-α) was used as a pathogenicity marker of the strains found followed by the sequencing of two products. Information on water management by aqueduct operators was collected in order to establish statistical relationships. Results: A total of 112 water samples were analyzed. Successful cultivation and molecular identification using the glmM marker was achieved in 39% of samples from areas of high incidence and in 7.5% of samples from areas of low incidence. Two glmM gene PCR products were sequenced and confirmed as true positives. Conclusions: The highest prevalence rate of Helicobacter pylori was found in water from areas with a high incidence of gastric cancer. Additionally, significant statistical correlations were established among environmental conditions, drinking water management and incidence of gastric cancer.展开更多
Helicobacter pylori is the microbial agent most responsible for gastro-duodenal ulcer and chronic gastritis, which can develop into carcinoma of the stomach. This study was performed in Wad Medani Teaching Hospital, S...Helicobacter pylori is the microbial agent most responsible for gastro-duodenal ulcer and chronic gastritis, which can develop into carcinoma of the stomach. This study was performed in Wad Medani Teaching Hospital, Sudan to detect Helicobacter pylori in stomach samples, and evaluate the performance of the tests used, which were histological stains and PCR. Gastric biopsies were obtained from 105 referred patients during endoscopy, and fixed specimens examined by haematoxylin-eosin and Warthin-Starry silver stains, while DNA was extracted for glmM gene amplification. Epigastric pain was the most common symptom at 78% (82/105) and chronic gastritis recorded with 71% (68/105) of endoscopy results. Warthin-Starry silver stain gave 31% (33/105) as positive for Helicobacter pylori followed by glmM gene 27% (28/105) and haematoxylin-eosin 24% (25/105). The study indicated good performance of histological staining and high specificity of glmM gene in detection of Helicobacter pylori from gastric biopsies.展开更多
In Streptococcus pyogenes, we have described the two-component signal transduction sensor and regulatory systems, CovR/S affect the antimicrobial susceptibility including penicillin G before. But the mechanism how two...In Streptococcus pyogenes, we have described the two-component signal transduction sensor and regulatory systems, CovR/S affect the antimicrobial susceptibility including penicillin G before. But the mechanism how two-component sensor protein CovS modulates penicillin G susceptibility has not been elucidated till date. This study aimed to determine how the CovS affected penicillin G susceptibility in Streptococcus pyogenes by northern blot analysis. At first, we investigated the covS mRNA expression under penicillin G induction. We found that the decrease of covS mRNA expression under Penicillin G stimulation. Next we investigated the expression of cell wall synthesis gene, pbp2a and glmM with use of covS knockout mutants from emm1 Streptococcus pyogenes strain 1529. We found that the cell-wall synthesis gene expression of the ?covS mutant strain were lower than that of the wild-type strain. Furthermore the expression of glmM mRNA gene was lower than the expression of pbp2a mRNA gene in the ?covS mutant strain. The covS-complemented strain almost restored the mRNA expression compared to covS mutant strain. The two-component sensor protein CovS affects the susceptibility to penicillin G in Streptococcus pyogenes by modulation of cell-wall synthesis.展开更多
The purpose of this study was to investigate whether the opinions of people eating together affect the taste of the foods they eat. In addition, if the opinions of others influence taste for one of the people eating w...The purpose of this study was to investigate whether the opinions of people eating together affect the taste of the foods they eat. In addition, if the opinions of others influence taste for one of the people eating with them, are the others’ opinions related to the empathy of individuals? Finally, this study was also intended to consider whether the taste threshold changes depending on the opinions of others. Twelve healthy young women (aged 18.4 ± 0.8 years;mean ± SD) participated in the present study. The participants tasted bread under three conditions: 1) quiet condition: a participant ate with three quiet persons, 2) positive condition: a participant ate with three persons who were talking favorably about taste, and 3) negative condition: a participant ate with three persons who were talking negatively about the taste. The electrical taste threshold was tested before and after tasting the bread, and a visual analog scale (VAS) was completed immediately after the tasting. Before the first trial, participants were asked to complete the Interpersonal Reactive Index (IRI). In the positive condition, the taste score increased significantly compared with the negative condition. There was no significant relationship between taste and empathic concern. To our knowledge, taste changed according to the comments of other people who were eating together. However, the change in taste due to the other’s speech was not related to the individual’s empathy. The results of the present study suggest that people experience food as delicious when others eating with them comment about the food being “delicious,” and this tendency did not depend on individuals’ empathy.展开更多
本文首次提出使用广义线性混合模型(generalized linear mixed model,GLMM)对概化理论(GT)和项目反应理论(IRT)进行统合,即在一次统计中就能同时获得GT和IRT所需要的估计结果。模拟研究结果显示:相比于传统的GT方差分量估计方法——期...本文首次提出使用广义线性混合模型(generalized linear mixed model,GLMM)对概化理论(GT)和项目反应理论(IRT)进行统合,即在一次统计中就能同时获得GT和IRT所需要的估计结果。模拟研究结果显示:相比于传统的GT方差分量估计方法——期望均值平方(expected mean squares,EMS),GLMM可以获得更准确的方差分量、概化系数(G系数)和可靠性系数(Φ系数)估计值;相对于传统Rasch模型,GLMM可以获得更准确的题目难度参数估计值。实证研究展示GLMM在实际心理测量数据分析中的应用。展开更多
Background:Seven out of ten hornbill species in the Philippines are threatened with extinction.Among these is the endangered Visayan Hornbill(Penelopides panini),found on the islands of Panay and Negros.Threatened by ...Background:Seven out of ten hornbill species in the Philippines are threatened with extinction.Among these is the endangered Visayan Hornbill(Penelopides panini),found on the islands of Panay and Negros.Threatened by habitat loss and hunting,its population size is thought to have declined from 1800 individuals 20 years ago to less than 1000.However,a recent study on Negros estimated 3564 individuals across three core forest blocks.This study aims to quantify the Visayan Hornbill population size in and around the Northwest Panay Peninsula Natural Park(NWPPNP)on Panay,the largest contiguous low-elevation forest landscape remaining across its range,and its broad habitat associations across a gradient of environmental degradation.Methods:Hornbills were surveyed using 10-min distance sampling point counts(n=367)along transects(average length 1.1 km).Environmental variables were recorded along transects,while habitat was classified into primary forest,secondary forest,plantation,or open habitat.Distance software was used to estimate population densities stratified by habitat,with the overall population estimate taken as a mean of habitat density estimates weighted by habitat area.Using generalized linear mixed models,hornbill occurrence was modelled using combinations of nine environmental variables as main and two-way fixed effects.Results:Surveys covered 204.4 km^(2) of the 374.8 km^(2) Northwest Panay Peninsula.Hornbills were not recorded in plantations or open habitats.Hornbill density was significantly higher in primary forest(17.8 individuals/km~2±26.9%CV)than in secondary forest(3.7 individuals/km^(2)±33.2%CV;z=15.212,P<0.001).The overall population estimate for the NWPPNP and environs is 2109 individuals,and 2673 individuals for the entire Northwest Panay Peninsula.Hornbill presence was best explained by a model including distance from the Park boundary alongside five interaction effects and transect as a random effect.Distance,and the interaction between distance and medium-sized trees were significant predi展开更多
基金This work was supported by the National Natural Science Foundation of China(32271551)the Metasequoia funding of Nanjing Forestry University.Conflict of interest statement.The authors declare that they have no conflict of interest.
文摘Generalized linear mixed models(GLMMs)have been widely used in contemporary ecology studies.However,determination of the relative importance of collinear predictors(i.e.fixed effects)to response variables is one of the challenges in GLMMs.Here,we developed a novel R package,glmm.hp,to decompose marginal R2^(2)explained by fixed effects in GLMMs.The algorithm of glmm.hp is based on the recently proposed approach‘average shared variance’i.e.used for multivariate analysis.We explained the principle and demonstrated the use of this package by simulated dataset.The output of glmm.hp shows individual marginal R2^(2)s that can be used to evaluate the relative importance of predictors,which sums up to the overall marginal R2^(2).Overall,we believe the glmm.hp package will be helpful in the interpretation of GLMM outcomes.
文摘Background: Most patients infected with Helicobacter pylori show no clinical symptoms. Nonetheless, approximately 10% to 20% of these patients will develop peptic ulcers and 1% will develop gastric cancer. The International Agency for Cancer Research has classified Helicobacter pylori as a Group 1 carcinogen. Materials and Methods: Drinking water samples from 20 cantons situated in areas of low and high incidence of gastric cancer in Costa Rica were analyzed. Water samples were concentrated and the nitrocellulose filter was cultivated for later molecular identification of Helicobacter pylori using the glmM marker. The tumor necrosis factor-alpha inducing protein (Tipalpha TNF-α) was used as a pathogenicity marker of the strains found followed by the sequencing of two products. Information on water management by aqueduct operators was collected in order to establish statistical relationships. Results: A total of 112 water samples were analyzed. Successful cultivation and molecular identification using the glmM marker was achieved in 39% of samples from areas of high incidence and in 7.5% of samples from areas of low incidence. Two glmM gene PCR products were sequenced and confirmed as true positives. Conclusions: The highest prevalence rate of Helicobacter pylori was found in water from areas with a high incidence of gastric cancer. Additionally, significant statistical correlations were established among environmental conditions, drinking water management and incidence of gastric cancer.
文摘Helicobacter pylori is the microbial agent most responsible for gastro-duodenal ulcer and chronic gastritis, which can develop into carcinoma of the stomach. This study was performed in Wad Medani Teaching Hospital, Sudan to detect Helicobacter pylori in stomach samples, and evaluate the performance of the tests used, which were histological stains and PCR. Gastric biopsies were obtained from 105 referred patients during endoscopy, and fixed specimens examined by haematoxylin-eosin and Warthin-Starry silver stains, while DNA was extracted for glmM gene amplification. Epigastric pain was the most common symptom at 78% (82/105) and chronic gastritis recorded with 71% (68/105) of endoscopy results. Warthin-Starry silver stain gave 31% (33/105) as positive for Helicobacter pylori followed by glmM gene 27% (28/105) and haematoxylin-eosin 24% (25/105). The study indicated good performance of histological staining and high specificity of glmM gene in detection of Helicobacter pylori from gastric biopsies.
文摘In Streptococcus pyogenes, we have described the two-component signal transduction sensor and regulatory systems, CovR/S affect the antimicrobial susceptibility including penicillin G before. But the mechanism how two-component sensor protein CovS modulates penicillin G susceptibility has not been elucidated till date. This study aimed to determine how the CovS affected penicillin G susceptibility in Streptococcus pyogenes by northern blot analysis. At first, we investigated the covS mRNA expression under penicillin G induction. We found that the decrease of covS mRNA expression under Penicillin G stimulation. Next we investigated the expression of cell wall synthesis gene, pbp2a and glmM with use of covS knockout mutants from emm1 Streptococcus pyogenes strain 1529. We found that the cell-wall synthesis gene expression of the ?covS mutant strain were lower than that of the wild-type strain. Furthermore the expression of glmM mRNA gene was lower than the expression of pbp2a mRNA gene in the ?covS mutant strain. The covS-complemented strain almost restored the mRNA expression compared to covS mutant strain. The two-component sensor protein CovS affects the susceptibility to penicillin G in Streptococcus pyogenes by modulation of cell-wall synthesis.
文摘The purpose of this study was to investigate whether the opinions of people eating together affect the taste of the foods they eat. In addition, if the opinions of others influence taste for one of the people eating with them, are the others’ opinions related to the empathy of individuals? Finally, this study was also intended to consider whether the taste threshold changes depending on the opinions of others. Twelve healthy young women (aged 18.4 ± 0.8 years;mean ± SD) participated in the present study. The participants tasted bread under three conditions: 1) quiet condition: a participant ate with three quiet persons, 2) positive condition: a participant ate with three persons who were talking favorably about taste, and 3) negative condition: a participant ate with three persons who were talking negatively about the taste. The electrical taste threshold was tested before and after tasting the bread, and a visual analog scale (VAS) was completed immediately after the tasting. Before the first trial, participants were asked to complete the Interpersonal Reactive Index (IRI). In the positive condition, the taste score increased significantly compared with the negative condition. There was no significant relationship between taste and empathic concern. To our knowledge, taste changed according to the comments of other people who were eating together. However, the change in taste due to the other’s speech was not related to the individual’s empathy. The results of the present study suggest that people experience food as delicious when others eating with them comment about the food being “delicious,” and this tendency did not depend on individuals’ empathy.
文摘本文首次提出使用广义线性混合模型(generalized linear mixed model,GLMM)对概化理论(GT)和项目反应理论(IRT)进行统合,即在一次统计中就能同时获得GT和IRT所需要的估计结果。模拟研究结果显示:相比于传统的GT方差分量估计方法——期望均值平方(expected mean squares,EMS),GLMM可以获得更准确的方差分量、概化系数(G系数)和可靠性系数(Φ系数)估计值;相对于传统Rasch模型,GLMM可以获得更准确的题目难度参数估计值。实证研究展示GLMM在实际心理测量数据分析中的应用。
基金funded by the Mohamed bin Zayed Species Conservation Fund(project 192514132)Bristol Zoological SocietyDK was employed by Bristol Zoological Society to oversee the project,and HM,BT and AF worked as contractors for Bristol Zoological Society during the survey duration。
文摘Background:Seven out of ten hornbill species in the Philippines are threatened with extinction.Among these is the endangered Visayan Hornbill(Penelopides panini),found on the islands of Panay and Negros.Threatened by habitat loss and hunting,its population size is thought to have declined from 1800 individuals 20 years ago to less than 1000.However,a recent study on Negros estimated 3564 individuals across three core forest blocks.This study aims to quantify the Visayan Hornbill population size in and around the Northwest Panay Peninsula Natural Park(NWPPNP)on Panay,the largest contiguous low-elevation forest landscape remaining across its range,and its broad habitat associations across a gradient of environmental degradation.Methods:Hornbills were surveyed using 10-min distance sampling point counts(n=367)along transects(average length 1.1 km).Environmental variables were recorded along transects,while habitat was classified into primary forest,secondary forest,plantation,or open habitat.Distance software was used to estimate population densities stratified by habitat,with the overall population estimate taken as a mean of habitat density estimates weighted by habitat area.Using generalized linear mixed models,hornbill occurrence was modelled using combinations of nine environmental variables as main and two-way fixed effects.Results:Surveys covered 204.4 km^(2) of the 374.8 km^(2) Northwest Panay Peninsula.Hornbills were not recorded in plantations or open habitats.Hornbill density was significantly higher in primary forest(17.8 individuals/km~2±26.9%CV)than in secondary forest(3.7 individuals/km^(2)±33.2%CV;z=15.212,P<0.001).The overall population estimate for the NWPPNP and environs is 2109 individuals,and 2673 individuals for the entire Northwest Panay Peninsula.Hornbill presence was best explained by a model including distance from the Park boundary alongside five interaction effects and transect as a random effect.Distance,and the interaction between distance and medium-sized trees were significant predi
