Review of Applied Spatial Data Analysis with R by R. S. Bivand, E. J. Pebesma, and V. Gomez-Rubio

Most authors struggle to pick a title that adequately conveys all of the material covered in a book. When I first saw Applied Spatial Data Analysis with R, I expected a review of spatial statistical models and their applications in packages (libraries) from the CRAN site of R. The authors’ title is not misleading, but I was very pleasantly surprised by how deep the word “applied” is here. The first half of the book essentially covers how R handles spatial data. To some statisticians this may be boring. Do you want, or need, to know the difference between S3 and S4 classes, how spatial objects in R are organized, and how various methods work on the spatial objects? A few years ago I would have said “no,” especially to the “want” part. Just let me slap my EXCEL spreadsheet into R and run some spatial functions on it. Unfortunately, the world is not so simple, and ultimately we want to minimize effort to get all of our spatial analyses accomplished. The first half of this book certainly convinced me that some extra effort in organizing my data into certain spatial class structures makes the analysis easier and less subject to mistakes. I also admit that I found it very interesting and I learned a lot.

Accounting for uncertainty in ecological analysis: the strengths and limitations of hierarchical statistical modeling

Analyses of ecological data should account for the uncertainty in the process(es) that generated the data. However, accounting for these uncertainties is a difficult task, since ecology is known for its complexity. Measurement and/or process errors are often the only sources of uncertainty modeled when addressing complex ecological problems, yet analyses should also account for uncertainty in sampling design, in model specification, in parameters governing the specified model, and in initial and boundary conditions. Only then can we be confident in the scientific inferences and forecasts made from an analysis. Probability and statistics provide a framework that accounts for multiple sources of uncertainty. Given the complexities of ecological studies, the hierarchical statistical model is an invaluable tool. This approach is not new in ecology, and there are many examples (both Bayesian and non-Bayesian) in the literature illustrating the benefits of this approach. In this article, we provide a baseline for concepts, notation, and methods, from which discussion on hierarchical statistical modeling in ecology can proceed. We have also planted some seeds for discussion and tried to show where the practical difficulties lie. Our thesis is that hierarchical statistical modeling is a powerful way of approaching ecological analysis in the presence of inevitable but quantifiable uncertainties, even if practical issues sometimes require pragmatic compromises.

A General Framework for the Analysis of Animal Resource Selection from Telemetry Data

We propose a general framework for the analysis of animal telemetry data through the use of weighted distributions. It is shown that several interpretations of resource selection functions arise when constructed from the ratio of a use and availability distribution. Through the proposed general framework, several popular resource selection models are shown to be special cases of the general model by making assumptions about animal movement and behavior. The weighted distribution framework is shown to be easily extended to readily account for telemetry data that are highly auto-correlated; as is typical with use of new technology such as global positioning systems animal relocations. An analysis of simulated data using several models constructed within the proposed framework is also presented to illustrate the possible gains from the flexible modeling framework. The proposed model is applied to a brown bear data set from southeast Alaska.

A Model-Based Approach for Making Ecological Inference from Distance Sampling Data

We consider a fully model-based approach for the analysis of distance sampling data. Distance sampling has been widely used to estimate abundance (or density) of animals or plants in a spatially explicit study area. There is, however, no readily available method of making statistical inference on the relationships between abundance and environmental covariates. Spatial Poisson process likelihoods can be used to simultaneously estimate detection and intensity parameters by modeling distance sampling data as a thinned spatial point process. A model-based spatial approach to distance sampling data has three main benefits: it allows complex and opportunistic transect designs to be employed, it allows estimation of abundance in small subregions, and it provides a framework to assess the effects of habitat or experimental manipulation on density. We demonstrate the model-based methodology with a small simulation study and analysis of the Dubbo weed data set. In addition, a simple ad hoc method for handling overdispersion is also proposed. The simulation study showed that the model-based approach compared favorably to conventional distance sampling methods for abundance estimation. In addition, the overdispersion correction performed adequately when the number of transects was high. Analysis of the Dubbo data set indicated a transect effect on abundance via Akaike’s information criterion model selection. Further goodness-of-fit analysis, however, indicated some potential confounding of intensity with the detection function.

Benefit Cost Scenarios of Potential Oral Rabies Vaccination for Skunks in California

Scenario-based analyses were computed for benefits and costs linked with hypothetical oral rabies vaccination (ORV) campaigns to contain or eliminate skunk-variant rabies in skunks (Mephitis mephitis) in California, USA. Scenario 1 assumed baiting eight zones (43,388 km2 total) that comprised 73% of known skunk rabies locations in the state. Scenario 2 also assumed baiting these eight zones, but further assumed that added benefits would result from preventing the spread of skunk-variant rabies into Los Angeles County, USA. Scenarios assumed a fixed bait cost ($1.24 each) but varied campaigns (one, two and three annual ORV applications), densities of baits (37.5/km2, 75/km2 and 150/km2), levels of prevention (50%, 75%, and 100%), and contingency expenditures if rabies recurred (20%, 40%, and 60% of campaign costs). Prorating potential annual benefits during a 12-yr time horizon yielded benefit-cost ratios (BCRs) between 0.16 and 2.91 and between 0.34 and 6.35 for Scenarios 1 and 2, respectively. Economic issues relevant to potentially managing skunk-variant rabies with ORV are discussed.

SCWDS BRIEFS: Volume 20, Number 2 (July 2004)

National Veterinary Services Laboratories in Ames, Iowa, confirmed vesicular stomatitis (VS) in horses at one premises in Texas. As of July 21, 2004, infected animals were identified on a total of 45 premises in Colorado (11), New Mexico (21), and Texas (13). These are the first reports of VS in livestock in the United States since the 1998 epizootic. SCWDS VS Studies Chronic Wasting Disease Developments: nearly 118,000 wild white-tailed deer, mule deer, and elk were tested in the United States from October 2002 to September 2003, with 592 animals testing positive for the CWD prion. More than $38,000,000 was spent by federal and state wildlife and animal health agencies on CWD-related activities during this same period. The Second International Chronic Wasting Disease Symposium, hosted by the Wisconsin Department of Natural Resources, will be held in Madison, Wisconsin, July 12-14, 2005. Crow Decoys Used in West Nile Virus Study Although Lyme disease caused by a spirochete bacterium, Borrelia burgdorferi, is relatively rare in the southeastern United States, a Lyme disease-like infection referred to as Southern Tick-Associated Rash Illness (STARI) and thought to be caused by Borrelia lonestari, has been recognized in people in this region. The Ohio Division of Wildlife joined SCWDS as an associate member beginning July 1, 2004. The Final Report of the 2003 Hemorrhagic Disease (HD) Surveillance project has been completed and distributed to all cooperators. New of Caroline Duffie, Robbie Edalgo and wife Jen, Clay George, Darrell Kavanaugh, Lynn Lewis-Weiss’s husband, Dr. Kevin Weiss, and Nate Mechlin. New SCWDS staff include Brian Chandler, Jay Cumbee, Ginger Goekjian, Bill Hamrick, Sabrina McGraw, Kerri Pedersen, and Ben Wilcox. Recent SCWDS Publications Available

International Consensus Guidelines for Nutrition Therapy in Pancreatitis

Guidelines for nutrition support in pancreatitis have been inconsistently adapted to clinical practice. The International Consensus Guideline Committee (ICGC) established a pancreatitis task force to review published guidelines for pancreatitis in nutrition support. A PubMed search using the terms pancreatitis, acute pancreatitis, chronic pancreatitis, nutrition support, parenteral nutrition, enteral nutrition, and guidelines was conducted for the period from January 1999 to May 2011. Eleven guidelines were identified for review. The ICGC used the following process to develop unified guideline statements: summarize the strength of evidence (grading) of the guidelines; establish level of evidence for ICGC statements as high, intermediate, and low; assign published guideline levels of evidence; and define an ICGC grading system. International Pancreatitis Guideline Grades were established as follows: platinum-high level of evidence and consistent agreement among the guidelines; gold-acceptable level of evidence and no conflicting statements in guidelines; and silver-single existing guideline statement with no conflict in other guidelines. Eighteen ICGC statements were derived from the 11 published pancreatitis guidelines. Uniform agreement from widely disparate groups (United States, Europe, Japan, and China) resulted in 4 platinum-level guideline statements for nutrition in pancreatitis: nutrition support therapy (NST) is generally not needed for mild to moderate disease, NST is needed for severe disease, enteral nutrition (EN) is preferred over parenteral nutrition (PN), and use PN when EN is contraindicated or not feasible. This methodology provides a template for future ICGC nutrition guideline development. (JPEN J Parenter Enteral Nutr. 2012;36:284-291)

THE ASSOCIATION BETWEEN CHILDHOOD ADVERSITY AND COMPONENTS OF METABOLIC SYNDROME IN ADULTS WITH MOOD DISORDERS: RESULTS FROM THE INTERNATIONAL MOOD DISORDERS COLLABORATIVE PROJECT

Objective: We sought to determine whether a reported history of childhood adversity is associated with components of the National Cholesterol Education Program Adult Treatment Panel III (NCEP-ATP-III)-defined metabolic syndrome in adults with mood disorders. Method: This was a cross-sectional analysis of adult outpatients (N = 373; n = 230 female, n = 143 male; mean age [SD] = 42.86 [14.43]) from the International Mood Disorders Collaborative Project (University of Toronto and Cleveland Clinic) with DSM-IV-defined major depressive disorder and bipolar I/II disorder. Childhood adversity was measured with the Klein Trauma & Abuse-Neglect self-report scale. The groups with and without childhood adversity were compared to determine possible differences in the rates of metabolic syndrome and its components. Logistic and linear regressions adjusted for age, sex, education, employment status, and smoking were used to evaluate the association between childhood adversity and components of metabolic syndrome. Results: For the full sample, 83 subjects (22.25%) met criteria for metabolic syndrome. Individuals reporting a history of any childhood adversity had higher systolic and diastolic blood pressure (systolic: p = 0.040; diastolic: p = 0.038). Among subjects with a history of sexual abuse, a significant proportion met criteria for obesity (45.28% vs. 32.88%; p = 0.010); a trend toward overweight was found for subjects with a history of physical abuse (76.32% vs. 63.33%; p = 0.074), although this relationship did not remain significant after adjusting for potential confounders. There was no statistically significant difference in the overall rate of dyslipidemia and/or metabolic syndrome between subjects with and without childhood adversity. Conclusion: The results herein provide preliminary evidence suggesting that childhood adversity is associated with metabolic syndrome components in individuals with mood disorders. Int'l. J. Psychiatry in Medicine 2012;43:165-177)

Predicting Growth of Panicum maximum: An Adaptation of the CROPGRO-Perennial Forage Model

Warm-season grasses are economically important for cattle production in tropical regions and tools to aid in management and research on these forages would be highly beneficial both in research and the industry. This research was conducted to adapt the CROPGRO-Perennial Forage model to simulate growth of the tropical species guineagrass (Panicum maximum Jacq. cv. 'Tanzania') and to describe model adaptation for this species. To develop the CROPGRO parameters for this species, we began with values and relationships reported in the literature. Some parameters and relationships were calibrated by comparison with observed growth, development, dry matter accumulation, and partitioning during a 17-mo experiment with Tanzania guineagrass in Piracicaba, SP, Brazil. Compared with starting parameters for palisadegrass [Brachiaria brizantha (A. Rich.) Stapf. cv. 'Xaraes'], dormancy effects of the perennial forage model had to be minimized, partitioning to storage tissue or root decreased, and partitioning to leaf and stem increased to provide for more leaf and stem growth and less root. Parameters affecting specific leaf area and senescence of plant tissues were improved. After these changes were made to the model, biomass accumulation was better simulated, mean predicted herbage yield was 6576 kg ha(-1), averaged across 11 regrowth cycles of 35 (summer) or 63 d (winter), with a RMSE of 494 kg ha(-1) (Willmott's index of agreement d = 0.985, simulated/observed ratio = 1.014). The model also gave good predictions against an independent data set, with similar RMSE, ratio, and d. The results of the adaptation suggest that the CROPGRO model is an efficient tool to integrate physiological aspects of guineagrass and can be used to simulate growth.

Population size of threatened and endemic birds of the Cerrado in Estacao Ecologica de Itirapina, a fragmented area in the State of Sao Paulo, Brazil

The pressures for land use change have led to an increasing isolation of habitat remnants throughout the world. The goal of this study was to estimate the population size and density of some endemic and threatened species in a nature reserve in the Cerrado biome. One hundred and thirty four point transects were undertaken at the Estacao Ecologica de Itirapina (EEI), one of the last natural grassland savannah remnants in Sao Paulo state, in the south-east of Brazil between September and December 2006 and densities estimated for seven species (four endemic to the Cerrado, one near-endemic and two grassland specialists). Neither species reached the minimum viable population size of 500-5000 individuals. Four species, White-banded Tanager, White-rumped Tanager, Black-throated Saltator and Sharp-tailed Tyrant have populations ranging from 112 to 248 individuals, while the other species have a low population (< 60 individuals). The mean densities of Sharp-tailed Tyrant and Cock-tailed Tyrant in the EEI grassland showed similar values to those observed in larger areas of the Cerrado, which may indicate that the EEL grassland area is well conserved. In spite of the restricted size of the EEI, small areas can maintain some endemic and threatened bird populations, thus contributing to local biodiversity and the ecological processes in the region. The capacity of fragments of Cerrado (similar to 2,000 ha) to maintain populations of endemic and threatened bird species is unlikely to be effective in the long term.

Functional characterisation of the non-essential protein kinases and phosphatases regulating Aspergillus nidulans hydrolytic enzyme production

Abstract Background Despite recent advances in the understanding of lignocellulolytic enzyme regulation, less is known about how different carbon sources are sensed and the signaling cascades that result in the adaptation of cellular metabolism and hydrolase secretion. Therefore, the role played by non-essential protein kinases (NPK) and phosphatases (NPP) in the sensing of carbon and/or energetic status was investigated in the model filamentous fungus Aspergillus nidulans. Results Eleven NPKs and seven NPPs were identified as being involved in cellulase, and in some cases also hemicellulase, production in A. nidulans. The regulation of CreA-mediated carbon catabolite repression (CCR) in the parental strain was determined by fluorescence microscopy, utilising a CreA: GFP fusion protein. The sensing of phosphorylated glucose, via the RAS signalling pathway induced CreA repression, while carbon starvation resulted in derepression. Growth on cellulose represented carbon starvation and derepressing conditions. The involvement of the identified NPKs in the regulation of cellulose-induced responses and CreA derepression was assessed by genome-wide transcriptomics (GEO accession 47810). CreA:GFP localisation and the restoration of endocellulase activity via the introduction of the ∆creA mutation, was assessed in the NPK-deficient backgrounds. The absence of either the schA or snfA kinase dramatically reduced cellulose-induced transcriptional responses, including the expression of hydrolytic enzymes and transporters. The mechanism by which these two NPKs controlled gene transcription was identified, as the NPK-deficient mutants were not able to unlock CreA-mediated carbon catabolite repression under derepressing conditions, such as carbon starvation or growth on cellulose. Conclusions Collectively, this study identified multiple kinases and phosphatases involved in the sensing of carbon and/or energetic status, while demonstrating the overlapping, synergistic roles of schA and snfA in the regulation of CreA derepression and hydrolytic enzyme production in A. nidulans. The importance of a carbon starvation-induced signal for CreA derepression, permitting transcriptional activator binding, appeared paramount for hydrolase secretion.

Avaliação da qualidade de vida após sinusectomia endoscópica para rinossinusite crônica

A rinossinusite crônica é uma doença de etiologia não definida que impacta significativamente a qualidade de vida dos pacientes. A sinusectomia endoscópica foi demonstrada como um tratamento eficaz em melhorar a qualidade de vida dos pacientes em outros países; contudo, não existem estudos nacionais. OBJETIVO: Avaliar a associação cirurgia endoscópica nasossinusal com a qualidade de vida doença-específica dos pacientes com rinossinusite crônica com e sem polipose nasossinusal pelo SNOT-20. Desenho: Estudo prospectivo. PACIENTES E MÉTODOS: Pacientes submetidos à sinusectomia endoscópica após ausência de melhora ao tratamento medicamentoso foram avaliados pelo questionário SNOT-20p antes e 12 meses após a cirurgia. Avaliou-se a melhora na pontuação total e nos cinco itens considerados mais importantes por cada paciente. Avaliamos também a presença de correlação entre a pontuação pré-operatória e a melhora pós-operatória e se havia diferença entre a melhora segundo sexo. RESULTADOS: Incluímos 43 pacientes com idade de 44 (19), md (IIQ); e 60,5% (26/43) do sexo masculino. Os pacientes apresentaram melhora estatisticamente significativa no SNOT-20 e SNOT-20 (5+), e correlação entre a pontuação pré-operatória e a melhora da pontuação (p<0.001). Não houve diferença entre melhora da pontuação na qualidade de vida segundo o sexo. CONCLUSÃO: A sinusectomia endoscópica em pacientes com rinossinusite crônica apresenta associação com melhora da QV doença-específica estatisticamente significativa.

Regiocontrolled Synthesis of Pyrazole Derivatives Through 1,3-Dipolar Cycloaddition Reaction And Synthesis of Helicene-Thiourea based and Polymer Supported Soos's Catalyst for Asymmetric Synthesis

In first part we have developed a simple regiocontrolled protocol of 1,3-DC to get ring fused pyrazole derivatives. These pyrazole derivatives were synthesized using 1,3-DC between nitrile imine and various dipolarophiles such as alkynes, cyclic α,β-ketones, lactones, thiocatones and lactums. The reactions were found to be highly regiospecific. In second part we have discussed about helicene, its properties, synthesis and applications as asymmetric catalyst.Due to inherent chirality, herein we have made an attempt to synthesize the helicene-thiourea based catalyst for asymmetric catalysis. The synthesis involved formation of two key intermediates viz, bromo-phenanthrene 5 and a vinyl-naphthalene 10. The coupling of these two intermediates leads to formation of hexahelicene.

(106)Ruthenium brachytherapy for ciliary recurrence with supraciliary effusion in retinoblastoma

A 2-year-old boy with syndromic bilateral retinoblastoma resulting from a (del(13)(q12.3q14.3)) developed a recurrent tumor measuring 2.3 X 2.3 mm at the ora serrata 15 months following last treatment.

Tumor lymphangiogenesis and metastasis to lymph nodes induced by cancer cell expression of podoplanin

The membrane glycoprotein podoplanin is expressed by several types of human cancers and might be associated with their malignant progression. Its exact biological function and molecular targets are unclear, however. Here, we assessed the relevance of tumor cell expression of podoplanin in cancer metastasis to lymph nodes, using a human MCF7 breast carcinoma xenograft model. We found that podoplanin expression promoted tumor cell motility in vitro and, unexpectedly, increased tumor lymphangiogenesis and metastasis to regional lymph nodes in vivo, without promoting primary tumor growth. Importantly, high cancer cell expression levels of podoplanin correlated with lymph node metastasis and reduced survival times in a large cohort of 252 oral squamous cell carcinoma patients. Based on comparative transcriptional profiling of tumor xenografts, we identified endothelin-1, villin-1, and tenascin-C as potential mediators of podoplanin-induced tumor lymphangiogenesis and metastasis. These unexpected findings identify a novel mechanism of tumor lymphangiogenesis and metastasis induced by cancer cell expression of podoplanin, suggesting that reagents designed to interfere with podoplanin function might be developed as therapeutics for patients with advanced cancer.