Multinomial Log-linear Models Research Articles

Evaluation of bias and gender/racial concordance based on sentiment analysis of narrative evaluations of clinical clerkships using natural language processing

There is increasing interest in understanding potential bias in medical education. We used natural language processing (NLP) to evaluate potential bias in clinical clerkship evaluations. Data from medical evaluations and administrative databases for medical students enrolled in third-year clinical clerkship rotations across two academic years. We collected demographic information of students and faculty evaluators to determine gender/racial concordance (i.e., whether the student and faculty identified with the same demographic). We used a multinomial log-linear model for final clerkship grades, using predictors such as numerical evaluation scores, gender/racial concordance, and sentiment scores of narrative evaluations using the SentimentIntensityAnalyzer tool in Python. 2037 evaluations from 198 students were analyzed. Statistical significance was defined as P < 0.05. Sentiment scores for evaluations did not vary significantly by student gender, race, or ethnicity (P = 0.88, 0.64, and 0.06, respectively). Word choices were similar across faculty and student demographic groups. Modeling showed narrative evaluation sentiment scores were not predictive of an honors grade (odds ratio [OR] 1.23, P = 0.58). Numerical evaluation average (OR 1.45, P < 0.001) and gender concordance between faculty and student (OR 1.32, P = 0.049) were significant predictors of receiving honors. The lack of disparities in narrative text in our study contrasts with prior findings from other institutions. Ongoing efforts include comparative analyses with other institutions to understand what institutional factors may contribute to bias. NLP enables a systematic approach for investigating bias. The insights gained from the lack of association between word choices, sentiment scores, and final grades show potential opportunities to improve feedback processes for students.

Per- and Polyfluoroalkyl Substances (PFAS) and Lipid Trajectories in Women 45-56 Years of Age: The Study of Women's Health Across the Nation.

Per- and polyfluoroalkyl substances (PFAS) are associated with less favorable blood lipid profiles in epidemiological studies. However, little is known about the potential role of PFAS in longitudinal changes in lipids among midlife women even though women become more susceptible to metabolic alterations during the menopausal transition. To examine associations of serum PFAS concentrations with longitudinal trajectories of blood total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, and triglycerides in midlife women undergoing menopausal transition. The sample included 1,130 women from the Study of Women's Health Across the Nation 45-56 y of age at baseline (1999-2000). We measured serum PFAS concentrations including linear perfluorooctanoic acid (n-PFOA), perfluorononanoic acid (PFNA), linear and branched perfluorooctanesulfonic acid (n-PFOS and Sm-PFOS, respectively), and perfluorohexanesulfonic acid (PFHxS) at baseline. We used k-means clustering to identify subgroups with different patterns of PFAS mixture. Blood lipids were measured annually or biannually through 2016 with an average follow-up of 14.8 y. We identified longitudinal trajectories of each lipid using latent class growth models. We used multinomial log-linear models adjusted for covariates to estimate odds ratios (ORs) and 95% confidence intervals (CIs) of lipid trajectory classes by PFAS and their mixtures. Three distinct trajectories (low, middle, high) of total, LDL, and HDL cholesterol and two distinct trajectories (low and high) of triglycerides were identified. n-PFOS, Sm-PFOS, and PFHxS were positively associated with total and LDL cholesterol trajectories. n-PFOS was inversely associated with triglycerides trajectories. PFAS mixtures (high vs. low) showed positive associations with total and LDL cholesterol trajectories (high vs. low), showing ORs (95% CIs) of 1.69 (95% CI: 1.36, 2.12) and 1.79 (95% CI: 1.44, 2.22), respectively. Concentrations of serum PFAS were positively associated with trajectories of total and LDL cholesterol, providing a line of evidence supporting adverse effects of PFAS on lipid homeostasis. https://doi.org/10.1289/EHP12351.

The brachycephalic paradox: The relationship between attitudes, demography, personality, health awareness, and dog-human eye contact

Brachycephalic (flat-faced) dogs’ popularity is rising worldwide despite the numerous health problems they often face. This is the brachycephalic paradox which led to a dog welfare crisis. To take meaningful steps in solving this crisis, we need to understand the appealing features of these dogs, and the characteristics of brachycephalic dog enthusiasts. We assumed that individuals who like these dogs have lower knowledge about the associated health problems, a unique personality profile, and highly value the tendency of these dogs to form eye contact with humans. We conducted an online survey with 1156 respondents. A Multinomial Log-linear Model was used to analyse respondents' attitudes towards brachycephalic dogs (positive, negative, or neutral), while a Binomial Generalized Linear Mixed-Effects Model was used to analyse their preference for eye contact with dogs. Some of the results were contrary to our expectations. People with a positive attitude towards brachycephalic dogs associated more health problems with brachycephalism and did not prefer photos of dogs making eye contact (looking into the camera) over those looking away. They were also found to be younger, more often women, have children, lower levels of education, a higher level of agreeableness, conscientiousness, and dog-directed emotional empathy. The results suggest that the tendency of brachycephalic dogs to form eye contact does not play a role in their popularity and that high emotional empathy and knowledge about health problems do not discourage people from liking these dogs. Our study can also serve as a basis for educational campaigns by demonstrating that factual knowledge about health problems alone is not enough to reverse the brachycephalic dog welfare crisis.

Non-linear change in body condition score over lifetime is associated with breed in dairy cows in Germany

Optimal body condition is crucial for the well-being and optimal productivity of dairy cows. However, body condition depends on numerous, often interacting factors, with complex relationships between them. Moreover, most of the studies describe the body condition in Holstein cattle, while condition of some breeds, e.g. Simmental (SIM) and Brown Swiss (BS) cattle, have not been intensively studied yet. Body condition score (BCS) proved to be one of the most effective measures for monitoring body condition in dairy cows. Alterations in BCS were previously mainly studied over a single lactation period, while changes over the lifetime were largely ignored. This study was designed to report BCS of German SIM and BS cows in the light of the broadly accepted BCS in German Holstein (GH) cows and to explore patterns of change in BCS over the productive lifetime of animals. BCS was modeled via linear mixed effects regression, over- and undercondition of animals were studied using mixed effects logistic regressions and condition of animals was explored with the multinomial log-linear model via neural networks. All models included an interaction between breed and age. We found BCS of SIM and BS to be higher than BCS of GH. Our results show that BCS of BS cows did not change over the lifetime. In contrast, the BCS of GH and SIM was found to have a non-linear (quadratic) shape, where BCS increased up to the years of highest productivity and then decreased in aging cows. Patterns of change between SIM and GH, however, differed. GH do not only reach their highest BCS earlier in life compared to SIM, but also start to lose their body condition earlier. Our dataset revealed that 23% of the animals scored were over- and 14% underconditioned. The proportion of cows that were overconditioned was high (>10% of cows) for every breed and every age, while severe underconditioning (>10% of cows) occurred only in middle aged and old GH. Moreover, we found that the probability of underconditioning of animals over lifetime increases, while the overconditioning decreases from the middle to older ages. Our findings highlight the importance of understanding the non-linear nature of BCS, and uncover the potential opportunity for improving the performance and welfare of dairy cows by adjusting their nutrition, not only during lactation, but also highly specific to breed and age.

Association of perfluoroalkyl substances (PFAS) with lipid trajectories in midlife women: the Study of Women&amp;#x27;s Health Across the Nation

BACKGROUND AND AIM: Despite lipid-lowering effects of perfluoroalkyl substances (PFAS) observed in rodent models, PFAS have been associated with unfavorable blood lipid profiles in human populations. However, evidence from longitudinal studies in the general population is limited. We examined the association of serum concentrations of PFAS with longitudinal trajectories of blood lipids in the Study of Women&amp;#x27;s Health Across the Nation. METHODS: We included 1143 women aged 45-56 years in 1999-2000. Concentrations of PFAS including linear and branched perfluorooctane sulfonic acid (n-PFOS and Sm-PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), and perfluorohexane sulfonic acid (PFHxS) were measured in serum collected at baseline. Total, low-density lipoprotein (LDL), and high-density lipoprotein (HDL) cholesterol, and triglycerides were measured in blood annually or biannually during follow-up through 2016. Using latent class growth models (LCGMs), trajectories of each lipid were estimated based on the population data. The associations between PFAS and lipid trajectory classes were evaluated by multinomial log-linear models with latent class membership as outcomes and log-transformed PFAS as exposure. RESULTS: Three distinct lipid trajectories (low, medium, and high trajectories) were identified. After adjustment for covariates, n-PFOS and Sm-PFOS were positively associated with higher LDL cholesterol [ORs (95% CI) for high vs. low trajectory per doubling of each PFAS: 1.28 (1.04, 1.56) and 1.24 (1.04, 1.48), respectively]. N-PFOS, n-PFOA, PFNA, and PFHxS were inversely associated with higher triglycerides [ORs (95% CIs) for high vs. low trajectory per doubling of each PFAS: 0.72 (0.55, 0.94), 0.65 (0.50, 0.84), 0.78 (0.62, 1.00), and 0.76 (0.62, 0.93), respectively]. The associations of PFAS with total or HDL cholesterol were insignificant. CONCLUSIONS: Higher serum concentrations of selected PFAS were associated with a higher trajectory of LDL cholesterol and a lower trajectory of triglycerides. Further studies on the underlying mechanisms of the findings are warranted. KEYWORDS: PFAS, dyslipidemia, midlife women

Prediction of desert locust breeding areas using machine learning methods and SMOS (MIR_SMNRT2) Near Real Time product

Despite satellite imagery is being used to identify suitable areas for desert locust, there is a lack of automatized and operational procedures in Near Real Time (NRT). The aim of this study was to assess the capacity of Soil Moisture Near Real Time Neural Network Level 2 product (MIR_SMNRT2) from the Soil Moisture and Ocean Salinity satellite (SMOS) to predict nymphs of desert locust. We used soil moisture time series (between 2016 and 2019) to build 6 machine learning models (logistic regression model “glm”, eXtreme Gradient Boosting “xgbTree”, Weighted k-Nearest Neighbors “kknn”, Feed-Forward Neural Networks and Multinomial Log-Linear Models “nnet”, support vector machine radial “svmRadial”, and random forest “rf”) over the entire recession area. Model results proved that spatial and/or temporal constraints in data sampling conditioned the predictive capacity of the selected machine learning algorithms. Furthermore, we used a forward selection procedure to evaluate the impact that time series data exert on modelling. Our results suggest that soil moisture data retrieved between 95 and 12 days (before the sighting) provided sufficient information to achieve acceptable predictive performances. This methodology can improve current preventive and control operations, it is site-specific, and could be used to other pests.

Genomic Association vs. Serological Determination of ABO Blood Types in a Chinese Cohort, with Application in Mendelian Randomization.

ABO blood system is an inborn trait determined by the ABO gene. The genetic-phenotypic mechanism underneath the four mutually exclusive and collectively exhaustive types of O, A, B and AB could theoretically be elucidated. However, genetic polymorphisms in the human populations render the link elusive, and importantly, past studies using genetically determined rather than biochemically determined ABO types were not and could not be evaluated for the inference errors. Upon both blood-typing and genotyping a cohort of 1008 people of the Han Chinese population, we conducted a genome-wide association study in parallel with both binomial and multinomial log-linear models. Significant genetic variants are all mapped to the ABO gene, and are quantitatively evaluated for binary and multi-class classification performances. Three single nucleotide polymorphisms of rs8176719, rs635634 and rs7030248 would together be sufficient to establish a multinomial predictive model that achieves high accuracy (0.98) and F1 scores (micro 0.99 and macro 0.97). Using the set of identified ABO-associated genetic variants as instrumental variables, we demonstrate the application in causal analysis by Mendelian randomization (MR) studies on blood pressures (one-sample MR) and severe COVID-19 with respiratory failure (two-sample MR).

Assessing the validity of an IAU General English Achievement Test through hybridizing differential item functioning and differential distractor functioning

The current study sought to examine the validity of a General English Achievement Test (GEAT), administered to university students in the fall semester of 2018–2019 academic year, by hybridizing differential information (DIF) and differential distractor function (DDF) analytical models. Using a purposive sampling method, from the target population of undergraduate students studying in different disciplines at Islamic Azad University (IAU), (Isfahan branch), a sample of 835 students taking GEAT were selected. The 60-item multiple-choice test comprised four sub-sections; namely, vocabulary, grammar, cloze test, and reading comprehension. The students’ test scores served as the targeted data and the validity of the test was examined through the application of Cochran-Mantel-Haenszel (CMH) and multinomial log-linear regression models for detecting DIF and DDF, respectively. To account for the assumption of uni-dimensionality, the test sub-sections were analyzed independently. Furthermore, the assumption of local independence was checked based on correlational analysis and no extreme values were observed. The results of the study identified five moderate-level DIF items and one DDF item signaling an adverse effect on test fairness due to the existing biased items. Notably, these findings may have important implications for both language policymakers and test developers.

Behavior traits associated with career outcome in a prison puppy-raising program

The Canine Behavioral Assessment and Research Questionnaire (C-BARQ©) (http://www.cbarq.org) has been used to measure behaviors associated with release or graduation from several assistance dog programs, however it has never been evaluated within a prison environment. This study investigated whether a modified version of the C-BARQ© can be utilized in a prison puppy-raising program (Puppies Behind Bars, PBB) to identify behaviors that are associated with dogs’ career outcomes. PBB dogs that successfully complete the program are placed as service dogs or explosives detection dogs (EDD). Dogs are released from the program as a result of behavioral or medical problems. The PBB program has more than one career outcome, facilitating an assessment of the C-BARQ© as a tool to identify specific working dog roles based on differences in C-BARQ© subscale scores. We examined the associations between subscale scores and career outcomes by comparing the scores of dogs with successful outcomes (service or EDD) with those released for behavioral reasons. We assessed the questionnaire’s application to the PBB setting and its ability to distinguish between outcomes. 314 paper copies of the C-BARQ© were completed by puppy raisers from seven correctional facilities in the New York area when their assigned dog was between 6 and 16 months old. Dogs that had successfully completed the PBB program or had been released due to behavioral issues were included, whereas dogs still in training and those released for medical reasons were excluded. A total of 271 completed C-BARQ© questionnaires were analyzed. Service dogs and EDDs were compared with released dogs to determine whether C-BARQ subscale scores were associated with outcome. Multinomial log-linear models containing one subscale score and fixed factors (age group, medical category, sex, neuter status within sex, the interaction between age group and medical category) and outcome as the dependent variable, were fitted for each subscale. Service dogs had lower stranger-directed aggression, owner-directed aggression, dog-directed aggression, dog-directed fear, dog rivalry, chasing, stranger-directed fear, and separation-related problems than released dogs. EDDs had lower trainability, dog-directed fear, dog rivalry, and attachment/attention-seeking behavior than released dogs. These findings suggest that some of the C-BARQ© subscales might be used in the future to predict outcomes for young dogs. Results show that the C-BARQ© can be applied to the PBB program; however, the omission of seven questions is recommended.

The Efficacy of Predictive Methods in Financial Statement Fraud

The existence and persistence of financial statement fraud (FSF) are detrimental to the financial health of global capital markets. A number of detective and predictive methods have been used to prevent, detect, and correct FSF, but their practicability has always been a big challenge for researchers and auditors, as they do not address real-world problems. In this paper, both supervised and unsupervised approaches are employed for analysing the financial data obtained from China’s stock market in detecting FSF. The variables used in this paper are 18 financial datasets, representing a fraud triangle. Additionally, this study examined the properties of five widely used supervised approaches, namely, multi-layer feed forward neural network (MFFNN), probabilistic neural network (PNN), support vector machine (SVM), multinomial log-linear model (MLM), and discriminant analysis (DA), applied in different real-life situations. The empirical results show that MFFNN yields the best classification results in detection of fraudulent data presented in financial statement. The outcomes of this study can be applied to different types of financial statement datasets, as they present a practical way for constructing predictive models using a combination of supervised and unsupervised approaches.

Aircraft Disturbance to Common Murres (Uria aalge) at a Breeding Colony in Central California, USA

Devil's Slide Rock, a rock sea stack on the central California coast near San Francisco, USA, hosts a Common Murre (Uria aalge) colony that was recently restored after it was extirpated in the mid-1980s. Since the late 1990s, low-flying aircraft have threatened the colony at Devil's Slide Rock. To assess variables contributing to Common Murre disturbance, multinomial log-linear models were constructed and evaluated using reproductive timing and aircraft characteristics for 7 years (2008–2014). The top model included seven variables (year, reproductive timing, time of day, aircraft type, aircraft category, aircraft altitude and aircraft lateral distance from Devil's Slide Rock) and the interaction effects between aircraft type and aircraft category, and between altitude and distance. The odds of disturbance varied temporally, with 2010, 2011, 2013 and 2014 exhibiting greater odds of disturbance than 2008. Disturbance response was more likely during the pre-egg lay period and post-chick hatch period than during incubation; 47%, 51%, and 40% of over-flights, respectively, resulted in agitation or flushing. Helicopters were more likely to cause disturbance than fixed-wing aircraft; 72% of helicopter over-flights and 39% of fixed-wing aircraft resulted in agitation or flushing. Flushing was more likely to occur at lower aircraft altitudes and closer lateral distances; all flushing from over-flights occurred below 305 m, and 91% of agitation events occurred below 305 m. These results support the need for measures to reduce over-flight disturbance of the Devil's Slide Rock colony.

Work Ability Trajectories and Retirement Pathways: A Longitudinal Analysis of Older American Workers.

Objective:To determine whether older workers who follow different work ability (WA) trajectories tend to follow different retirement pathways.Methods:Nationally representative data on Americans born between 1943 and 1948. Latent class growth modeling to estimate trajectories of work ability between ages 53–54 and 65–66. Multinomial log-linear models to assess the association between WA trajectories and retirement pathways.Results:Three WA trajectories were identified: high (74%), declining (17%), and low (9%). Low WA leads more often to an early-gradual retirement. Declining WA leads to both early-gradual and early-crisp retirements.Conclusions:Workers with low and declining WA are more at risk of unemployment, disability, and inactivity prior to retirement; workers with declining WA are also likely to make a direct transition to early retirement. Future changes to social security should consider inter-individual variation over time in WA.

Icing Detection over East Asia from Geostationary Satellite Data Using Machine Learning Approaches

Even though deicing or airframe coating technologies continue to develop, aircraft icing is still one of the critical threats to aviation. While the detection of potential icing clouds has been conducted using geostationary satellite data in the US and Europe, there is not yet a robust model that detects potential icing areas in East Asia. In this study, we proposed machine-learning-based icing detection models using data from two geostationary satellites—the Communication, Ocean, and Meteorological Satellite (COMS) Meteorological Imager (MI) and the Himawari-8 Advanced Himawari Imager (AHI)—over Northeast Asia. Two machine learning techniques—random forest (RF) and multinomial log-linear (MLL) models—were evaluated with quality-controlled pilot reports (PIREPs) as the reference data. The machine-learning-based models were compared to the existing models through five-fold cross-validation. The RF model for COMS MI produced the best performance, resulting in a mean probability of detection (POD) of 81.8%, a mean overall accuracy (OA) of 82.1%, and mean true skill statistics (TSS) of 64.0%. One of the existing models, flight icing threat (FIT), produced relatively poor performance, providing a mean POD of 36.4%, a mean OA of 61.0, and a mean TSS of 9.7%. The Himawari-8 based models also produced performance comparable to the COMS models. However, it should be noted that very limited PIREP reference data were available especially for the Himawari-8 models, which requires further evaluation in the future with more reference data. The spatio-temporal patterns of the icing areas detected using the developed models were also visually examined using time-series satellite data.

Spatial clustering of Borrelia burgdorferi sensu lato within populations of Allen's chipmunks and dusky-footed woodrats in northwestern California.

The ecology of Lyme borreliosis is complex in northwestern California, with several potential reservoir hosts, tick vectors, and genospecies of Borrelia burgdorferi sensu lato. The primary objective of this study was to determine the fine-scale spatial distribution of different genospecies in four rodent species, the California ground squirrel (Otospermophilus beecheyi), northern flying squirrel (Glaucomys sabrinus), dusky-footed woodrat (Neotoma fuscipes), and Allen’s chipmunk (Neotamias senex). Rodents were live-trapped between June 2004 and May 2005 at the Hoopa Valley Tribal Reservation (HVTR) in Humboldt County, California. Ear-punch biopsies obtained from each rodent were tested by polymerase chain reaction (PCR) and sequencing analysis. The programs ArcGIS and SaTScan were used to examine the spatial distribution of genospecies. Multinomial log-linear models were used to model habitat and host-specific characteristics and their effect on the presence of each borrelial genospecies. The Akaike information criterion (AICc) was used to compare models and determine model fit. Borrelia burgdorferi sensu stricto was primarily associated with chipmunks and B. bissettiae largely with woodrats. The top model included the variables “host species”, “month”, and “elevation” (weight = 0.84). Spatial clustering of B. bissettiae was detected in the northwestern section of the HVTR, whereas B. burgdorferi sensu stricto was clustered in the southeastern section. We conclude that the spatial distribution of these borreliae are driven at least in part by host species, time-of-year, and elevation.

Assessing the outcomes of mini-Monoka stent dilatation for primary punctal stenosis using the lacrimal symptom questionnaire.

Purpose:The objective of this study was to assess the quality of outcomes of mini-Monoka stent dilatation for punctal stenosis using the lacrimal symptom (Lac-Q) questionnaire.Methods:Prospective interventional case series of 45 eyes of 25 consecutive patients who underwent mini-Monoka stent dilatation for primary punctal stenosis were included in the study. The stents were extubated at 4 weeks. The Lac-Q questionnaire was administered preoperatively and at 12 weeks and 24 weeks following the intervention. Outcomes assessed were anatomical success, functional success, and changes in the questionnaire scores including total, social impact, and lacrimal symptom scores. Statistical analysis was performed using the Wilcoxon signed-rank test, and the probability of obtaining a certain score was calculated using the multinomial log-linear model. P < 0.05 was considered as significant.Results:Monoka stents were performed for 45 eyes. A total of 75 questionnaire responses were analyzed. At the last follow-up of 24 weeks, the anatomical and functional success rates were 93.3% (42/45). The changes in the mean total score (7.68 preoperatively to 0.82 at 24-week follow-up) were statistically significant (P ≤ 0.001). The mean social impact scores showed significant improvement postoperatively from 4.06 to 0.53 (P ≤ 0.001). The mean lacrimal symptom score changed from a preoperative value of 3.62 to 0.28 (P ≤ 0.001) at the last follow-up. Postoperative scoring correlated well with the anatomical and functional success rates. The symptom scores corroborated with changes in the clinical outcomes.Conclusion:Mini-Monoka stent dilatation is a very effective intervention for the management of primary punctal stenosis, and Lac-Q questionnaire is a simple and useful tool to evaluate the quality of outcomes in such cases.

Winter Space Partitioning of Woodpeckers and Nuthatches in Wisconsin

Abstract Woodpeckers and nuthatches are resident species sharing similar year-round habitat in northeastern North America, but little is known about how these species distribute themselves within the same wintering area. From 2009 to 2015, we conducted a mark—recapture study of 7 Downy Woodpeckers, 15 Hairy Woodpeckers, 9 Red-bellied Woodpeckers, and 39 White-breasted Nuthatches to determine geographical winter home-range partitioning between and within species. We used multinomial log-linear models to estimate the likelihood of capturing each species in a particular baited trap when other species had been caught in the same trap during the same year. Our results show the presence of each species influenced the likelihood at least 1 other species would inhabit the same area. Most of these relationships were positive and indicate active sharing of the same space. However, Hairy Woodpeckers appeared to deter White-breasted Nuthatches, and Red-bellied Woodpeckers avoided conspecifics. Little evidence of spac...

Driver Vision Based Perception-Response Time Prediction and Assistance Model on Mountain Highway Curve

To make driving assistance system more humanized, this study focused on the prediction and assistance of drivers’ perception-response time on mountain highway curves. Field tests were conducted to collect real-time driving data and driver vision information. A driver-vision lane model quantified curve elements in drivers’ vision. A multinomial log-linear model was established to predict perception-response time with traffic/road environment information, driver-vision lane model, and mechanical status (last second). A corresponding assistance model showed a positive impact on drivers’ perception-response times on mountain highway curves. Model results revealed that the driver-vision lane model and visual elements did have important influence on drivers’ perception-response time. Compared with roadside passive road safety infrastructure, proper visual geometry design, timely visual guidance, and visual information integrality of a curve are significant factors for drivers’ perception-response time.

Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests.

Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

Global pharmacogenomics: distribution of CYP3A5 polymorphisms and phenotypes in the Brazilian population.

The influence of self-reported “race/color”, geographical origin and genetic ancestry on the distribution of three functional CYP3A5 polymorphisms, their imputed haplotypes and inferred phenotypes was examined in 909 healthy, adult Brazilians, self-identified as White, Brown or Black (“race/color” categories of the Brazilian census). The cohort was genotyped for CYP3A5*3 (rs776746), CYP3A5*6 (rs10264272) and CYP3A5*7 (rs41303343), CYP3A5 haplotypes were imputed and CYP3A5 metabolizer phenotypes were inferred according to the number of defective CYP3A5 alleles. Estimates of the individual proportions of Amerindian, African and European ancestry were available for the entire cohort. Multinomial log-linear regression models were applied to infer the statistical association between the distribution of CYP3A5 alleles, haplotypes and phenotypes (response variables), and self-reported Color, geographical region and ancestry (explanatory variables). We found that Color per se or in combination with geographical region associates significantly with the distribution of CYP3A5 variant alleles and CYP3A5 metabolizer phenotypes, whereas geographical region per se influences the frequency distribution of CYP3A5 variant alleles. The odds of having the default CYP3A5*3 allele and the poor metabolizer phenotype increases continuously with the increase of European ancestry and decrease of African ancestry. The opposite trend is observed in relation to CYP3A5*6, CYP3A5*7, the default CYP3A5*1 allele, and both the extensive and intermediate phenotypes. No significant effect of Amerindian ancestry on the distribution of CYP3A5 alleles or phenotypes was observed. In conclusion, this study strongly supports the notion that the intrinsic heterogeneity of the Brazilian population must be acknowledged in the design and interpretation of pharmacogenomic studies, and dealt with as a continuous variable, rather than proportioned in arbitrary categories that do not capture the diversity of the population. The relevance of this work extrapolates the Brazilian borders, and extends to other admixed peoples of the Americas, with ancestral roots in Europe, Africa and the American continent.

Poisson loglinear modeling with linear constraints on the expected cell frequencies

In this paper we consider Poisson loglinear models with linear constraints (LMLC) on the expected table counts. Multinomial and product multinomial loglinear models can be obtained by considering that some marginal totals (linear constraints on the expected table counts) have been prefixed in a Poisson loglinear model. Therefore with the theory developed in this paper, multinomial and product multinomial loglinear models can be considered as a particular case. To carry out inferences on the parameters in the LMLC an information-theoretic approach is followed from which the classical maximum likelihood estimators and Pearson chi-square statistics for goodness-of fit are obtained. In addition, nested hypotheses are proposed as a general procedure for hypothesis testing. Through a simulation study the appropriateness of proposed inference tools is illustrated.