bluuebunny/crossref_metadata_2025 huggingface dataset:
Mammoth and Elephant Phylogenetic Relationships: Mammut Americanum, the Missing Outgroup
Authors: Orlando Ludovic , Hänni Catherine , Douady Christophe J.
Published: November 2017

At the morphological level, the woolly mammoth has most often been considered as the sister-species of Asian elephants, but at the DNA level, different studies have found support for proximity with African elephants. Recent reports have increased the available sequence data and apparently solved the discrepancy, finding mammoths to be most closely related to Asian elephants. However, we demonstrate here that the three competing topologies have similar likelihood, bayesian and parsimony supports. The analysis further suggests the inadequacy of using Sirenia or Hyracoidea as outgroups. We therefore argue that orthologous sequences from the extinct American mastodon will be required to definitively solve this long-standing question.
Minimizing Contradictions on Circular Order of Phylogenic Trees
Authors: Thuillard Marc
Published: November 2017

Distance-based approaches to phylogeny use estimations of the evolutionary distance between sequences to reconstruct an evolution tree. If the evolution can be represented by an X-tree, the different sequences can be ordered so that the distance matrix [Formula: see text], representing the distance from a leaf n to the path ( i, j), is perfectly ordered meaning that [Formula: see text] and [Formula: see text] For i ≤ j ≤ k. After ordering of the sequences, the distance matrix [Formula: see text] permits to visualize phylogenetic relationships between taxa and to localize deviations from perfect order. The effect of perturbations resulting from lateral gene transfer or crossover can be modeled probabilistically. The order is shown to be quite robust against many perturbations. We have developed algorithms to minimize the level of contradiction in the order of the sequences. These algorithms are tested on the SSU rRNA data for Archaea. The degree of contradiction after optimization is for most taxa quite low. Regions in the taxa space with deviations from perfect order were identified.
An Improved Implementation of Codon Adaptation Index
Authors: Xia Xuhua
Published: November 2017

Codon adaptation index is a widely used index for characterizing gene expression in general and translation efficiency in particular. Current computational implementations have a number of problems leading to various systematic biases. I illustrate these problems and provide a better computer implementation to solve these problems. The improved CAI can predict protein production better than CAI from other commonly used implementations.
Examining Ancient Inter-domain Horizontal Gene Transfer
Authors: Almeida Francisca C. , Leszczyniecka Magdalena , Fisher Paul B. , DeSalle Rob
Published: November 2017

Details of the genomic changes that occurred in the ancestors of Eukarya, Archaea and Bacteria are elusive. Ancient interdomain horizontal gene transfer (IDHGT) amongst the ancestors of these three domains has been difficult to detect and analyze because of the extreme degree of divergence of genes in these three domains and because most evidence for such events are poorly supported. In addition, many researchers have suggested that the prevalence of IDHGT events early in the evolution of life would most likely obscure the patterns of divergence of major groups of organisms let alone allow the tracking of horizontal transfer at this level. In order to approach this problem, we mined the E. coli genome for genes with distinct paralogs. Using the 1,268 E. coli K-12 genes with 40% or higher similarity level to a paralog elsewhere in the E. coli genome we detected 95 genes found exclusively in Bacteria and Archaea and 86 genes found in Bacteria and Eukarya. These genes form the basis for our analysis of IDHGT. We also applied a newly developed statistical test (the node height test), to examine the robustness of these inferences and to corroborate the phylogenetically identified cases of ancient IDHGT. Our results suggest that ancient inter domain HGT is restricted to special cases, mostly involving symbiosis in eukaryotes and specific adaptations in prokaryotes. Only three genes in the Bacteria + Eukarya class (Deoxyxylulose-5-phosphate synthase (DXPS), fructose 1,6-phosphate aldolase class II protein and glucosamine-6-phosphate deaminase) and three genes–in the Bacteria + Archaea class (ABC-type FE3+ -siderophore transport system, ferrous iron transport protein B, and dipeptide transport protein) showed evidence of ancient IDHGT. However, we conclude that robust estimates of IDHGT will be very difficult to obtain due to the methodological limitations and the extreme sequence saturation of the genes suspected of being involved in IDHGT.
The ABCs of MGR with DCJ
Authors: Adam Zaky , Sankoff David
Published: November 2017

We study the small phylogeny problem in the space of multichromosomal genomes under the double cut and join metric. This is similar to the existing MGR (multiple genome rearrangements) approach but it allows, in addition to inversion and reciprocal translocation, operations of transposition and block interchange. Empirically, with chloroplast and mammalian data sets, it finds solutions as good as or better than MGR when the latter operations are prohibited. Permitting these operations allows quantitatively better solutions where part of the reconstructed ancestral genomes may be included in circular chromosomes. We discuss the biological likelihood of transpositions and block interchanges in the mammalian data.
The Effect of Aromatic Hydrocarbon Receptor on the Phenotype of the Hepa 1c1c7 Murine Hepatoma Cells in the Absence of Dioxin
Authors: Wang Feng , Zhang Ruixue , Shi Shengli , Hankinson Oliver
Published: November 2017

The aromatic hydrocarbon receptor (AhR) mediates biological responses to certain exogenous ligands, such as the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and has also been demonstrated to modulate the cell cycle and differentiated state of several cell lines independently of exogenous ligands. In this study, we used DNA micorarray analysis to elucidate the profile of genes responsive to the expression of unliganded AhR by re-introducing AhR into an AhR-deficient mouse derivative (c19) of the mouse hepatoma cell line Hepa1c1c7. 22 gene products were up-regulated and 8 were down-regulated two-fold or more in c19 cells infected with a retroviral vector expressing mouse AhR. Surprisingly, expression of genes involved in cell proliferation or differentiation were not affected by introduction of AhR. AhR also did not restore expression of the albumin gene in c19 cells. Introduction of AhR into c12, a similar AhR-defective mouse hepatoma cell line, also did not restore albumin expression, and furthermore, did not lead to changes in cellular morphology or cell cycle parameters. These observations fail to support the notion that unliganded AhR regulates proliferation and differentiation of liver-derived cells.
Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome
Authors: Van Belle Werner , Gerits Nancy , Jakobsen Kirsti , Brox Vigdis , Van Ghelue Marijke , Moens Ugo
Published: November 2017

To perform a quantitative analysis with gene-arrays, one must take into account inaccuracies (experimental variations, biological variations and other measurement errors) which are seldom known. In this paper we investigated amplification and noise propagation related errors by measuring intensity dependent variations. Based on a set of control samples, we create confidence intervals for up and down regulations. We validated our method through a qPCR experiment and compared it to standard analysis methods (including loess normalization and filtering methods based on genetic variability). The results reveal that amplification related errors are a major concern.
Computational Systems Biology in Cancer: Modeling Methods and Applications
Authors: Materi Wayne , Wishart David S.
Published: November 2017

In recent years it has become clear that carcinogenesis is a complex process, both at the molecular and cellular levels. Understanding the origins, growth and spread of cancer, therefore requires an integrated or system-wide approach. Computational systems biology is an emerging sub-discipline in systems biology that utilizes the wealth of data from genomic, proteomic and metabolomic studies to build computer simulations of intra and intercellular processes. Several useful descriptive and predictive models of the origin, growth and spread of cancers have been developed in an effort to better understand the disease and potential therapeutic approaches. In this review we describe and assess the practical and theoretical underpinnings of commonly-used modeling approaches, including ordinary and partial differential equations, petri nets, cellular automata, agent based models and hybrid systems. A number of computer-based formalisms have been implemented to improve the accessibility of the various approaches to researchers whose primary interest lies outside of model development. We discuss several of these and describe how they have led to novel insights into tumor genesis, growth, apoptosis, vascularization and therapy.
CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling
Authors: Gu Joyce Xiuweu-Xu , Wei Michael Yang , Rao Pulivarthi H. , Lau Ching C. , Behl Sanjiv , Man Tsz-Kwong
Published: November 2017

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.
New Insights into the Genetic Regulation of Plasmodium Falciparum Obtained by Bayesian Modeling
Authors: Bulashevska Svetlana , Adebiyi Ezekiel , Brors Benedikt , Eils Roland
Published: November 2017

The most fatal and prevalent form of malaria is caused by the bloodborne pathogen Plasmodium falciparum (henceforth P.f). Annually, approximately three million people died of malaria. Despite P.f devastivating effect globally, the vast majority of its proteins have not been characterized experimentally. In this work, we provide computational insight that explore the modalities of the regulation for some important group of genes of P.f, namely components of the glycolytic pathway, and those involved in apicoplast metabolism. Glycolysis is a crucial pathway in the maintenance of the parasite while the recently discovered apicoplast contains a range of metabolic pathways and housekeeping processes that differ radically to those of the host, which makes it ideal for drug therapy.

We have been able to validate some of our findings from available literature and therefore provide a basis to give theoretical insight for some genes regulations, which has not been characterized experimentally.
The Role and Regulation of Receptor-Like Kinases in Plant Defense
Authors: Goff Kerry E. , Ramonell Katrina M.
Published: November 2017

Receptor-like kinases (RLKs) in plants are a large superfamily of proteins that are structurally similar. RLKs are involved in a diverse array of plant responses including development, growth, hormone perception and the response to pathogens. Current studies have focused attention on plant receptor-like kinases as an important class of sentinels acting in plant defense responses. RLKs have been identified that act in both broad-spectrum, elicitor-initiated defense responses and as dominant resistance (R) genes in race-specific pathogen defense. Most defense-related RLKs are of the leucine-rich repeat (LRR) subclass although new data are highlighting other classes of RLKs as important players in defense responses. As our understanding of RLK structure, activation and signaling has expanded, the role of the ubiquitin/proteasome system in the regulation of these receptors has emerged as a central theme.
β1-Integrin Signaling is Essential for Lens Fiber Survival
Authors: Samuelsson Andrew R. , Belvindrah Richard , Wu Chuanyue , Müller Uli , Halfter Willi
Published: November 2017

Integrins have been proposed to play a major role in lens morphogenesis. To determine the role of β1-integrin and its down-stream signaling partner, integrin linked kinase (ILK), in lens morphogenesis, eyes of WT mice and mice with a nestin-linked conditional knockout of β1-integrin or ILK were analyzed for defects in lens development. Mice, lacking the genes encoding the p1-integrin subunit ( Itgb1) or ILK ( Ilk), showed a perinatal degeneration of the lens. Early signs of lens degeneration included vacuolization, random distribution of lens cell nuclei, disrupted fiber morphology and attenuation and separation of the lens capsule. The phenotype became progressively more severe during the first postnatal week eventually leading to the complete loss of the lens. A more severe phenotype was observed in ILK mutants at similar stages. Eyes from embryonic day 13 β1-integrin-mutant embryos showed no obvious signs of lens degeneration, indicating that mutant lens develops normally until peri-recombination. Our findings suggest that β1-integrins and ILK cooperate to control lens cell survival and link lens fibers to the surrounding extracellular matrix. The assembly and integrity of the lens capsule also appears to be reliant on integrin signaling within lens fibers. Extrapolation of these results indicates a novel role of integrins in lens cell-cell adhesions as well as a potential role in the pathogenesis of congenital cataracts.
Transcription Initiation by Mix and Match Elements: Flexibility for Polymerase Binding to Bacterial Promoters
Authors: Hook-Barnard India G. , Hinton Deborah M.
Published: November 2017

Bacterial RNA polymerase is composed of a core of subunits (β β′, α1, α2, ω), which have RNA synthesizing activity, and a specificity factor (σ), which identifies the start of transcription by recognizing and binding to sequence elements within promoter DNA. Four core promoter consensus sequences, the –10 element, the extended –10 (TGn) element, the –35 element, and the UP elements, have been known for many years; the importance of a nontemplate G at position -5 has been recognized more recently. However, the functions of these elements are not the same. The AT-rich UP elements, the –35 elements (–35TTGACA–30), and the extended –10 (15TGn–13) are recognized as double-stranded binding elements, whereas the –5 nontemplate G is recognized in the context of single-stranded DNA at the transcription bubble. Furthermore, the –10 element (–12TATAAT–7) is recognized as both double-stranded DNA for the T:A bp at position –12 and as nontemplate, single-stranded DNA from positions –11 to –7. The single-stranded sequences at positions –11 to –7 as well as the –5 contribute to later steps in transcription initiation that involve isomerization of polymerase and separation of the promoter DNA around the transcription start site. Recent work has demonstrated that the double-stranded elements may be used in various combinations to yield an effective promoter. Thus, while some minimal number of contacts is required for promoter function, polymerase allows the elements to be mixed and matched. Interestingly, which particular elements are used does not appear to fundamentally alter the transcription bubble generated in the stable complex. In this review, we discuss the multiple steps involved in forming a transcriptionally competent polymerase/promoter complex, and we examine what is known about polymerase recognition of core promoter elements. We suggest that considering promoter elements according to their involvement in early (polymerase binding) or later (polymerase isomerization) steps in transcription initiation rather than simply from their match to conventional promoter consensus sequences is a more instructive form of promoter classification.
Gene Module Identification from Microarray Data Using Nonnegative Independent Component Analysis
Authors: Gong Ting , Xuan Jianhua , Wang Chen , Li Huai , Hoffman Eric , Clarke Robert , Wang Yue
Published: November 2017

Genes mostly interact with each other to form transcriptional modules for performing single or multiple functions. It is important to unravel such transcriptional modules and to determine how disturbances in them may lead to disease. Here, we propose a non-negative independent component analysis (nICA) approach for transcriptional module discovery. nICA method utilizes the non-negativity constraint to enforce the independence of biological processes within the participated genes. In such, nICA decomposes the observed gene expression into positive independent components, which fits better to the reality of corresponding putative biological processes. In conjunction with nICA modeling, visual statistical data analyzer (VISDA) is applied to group genes into modules in latent variable space. We demonstrate the usefulness of the approach through the identification of composite modules from yeast data and the discovery of pathway modules in muscle regeneration.
Early Onset of Heat-Shock Response in Mouse Embryos Revealed by Quantification of Stress-Inducible hsp70i RNA
Authors: Hartshorn Cristina , Anshelevich Aleksandra , Jia Yanwei , Wangh Lawrence J.
Published: November 2017

Heat shock response is fully established in mouse embryos at the blastocyst stage, but it is unclear when this response first arises during development. To shed light on this question, we used a single-tube method to quantify mRNA levels of the heat shock protein genes hsp70.1 and hsp70.3 ( hsp70i) in individual cleavage-stage embryos that had or had not been heat-shocked. While untreated, healthy embryos contained very low copy numbers of hsp70i RNA, heat shock rapidly induced the synthesis of hundreds of hsp70i transcripts per blastomere at both the 4-cell and the 8-cell stages. In addition, we performed hsp70i measurements in embryos that had not been heat-shocked but had been very slow in developing. Quantification of hsp70i RNA and genomic DNA copy numbers in these slow-growing embryos demonstrated the presence of two distinct populations. Some of the embryos contained considerable levels of hsp70i RNA, a finding consistent with the hypothesis of endogenous metabolic stress accompanied by cell cycle arrest and delayed development. Other slow-growing embryos contained no hsp70i RNA and fewer than expected hsp70i gene copies, suggesting the possibility of ongoing apoptosis. In conclusion, this study demonstrates that mouse embryos can activate hsp70i expression in response to sub-lethal levels of stress as early as at the 4-cell stage. Our results also indicate that quantification of hsp70i DNA and RNA copy numbers may provide a diagnostic tool for embryonic health.
Pharmacodynamic Modeling of Acute and Chronic Effects of Methylprednisolone on Hepatic Urea Cycle Genes in Rats
Authors: Hazra Anasuya , DuBois Debra C. , Almon Richard R. , Snyder Grayson H. , Jusko William J.
Published: November 2017

Corticosteroids (CS) regulate many enzymes at both mRNA and protein levels. This study used microarrays to broadly assess regulation of various genes related to the greater urea cycle and employs pharmacokinetic/pharmacodynamic (PK/PD) modeling to quantitatively analyze and compare the temporal profiles of these genes during acute and chronic exposure to methylprednisolone (MPL). One group of adrenalectomized male Wistar rats received an intravenous bolus dose (50 mg/kg) of MPL, whereas a second group received MPL by a subcutaneous infusion (Alzet osmotic pumps) at a rate of 0.3 mg/kg/hr for seven days. The rats were sacrificed at various time points over 72 hours (acute) or 168 hours (chronic) and livers were harvested. Total RNA was extracted and Affymetrix® gene chips (RGU34A for acute and RAE 230A for chronic) were used to identify genes regulated by CS. Besides five primary urea cycle enzymes, many other genes related to the urea cycle showed substantial changes in mRNA expression. Some genes that were simply up- or down-regulated after acute MPL showed complex biphasic patterns upon chronic infusion indicating involvement of secondary regulation. For the simplest patterns, indirect response models were used to describe the nuclear steroid-bound receptor mediated increase or decrease in gene transcription (e.g. tyrosine aminotransferase, glucocorticoid receptor). For the biphasic profiles, involvement of a secondary biosignal was assumed (e.g. ornithine decarboxylase, CCAAT/enhancer binding protein) and more complex models were derived. Microarrays were used successfully to explore CS effects on various urea cycle enzyme genes. PD models presented in this report describe testable hypotheses regarding molecular mechanisms and quantitatively characterize the direct or indirect regulation of various genes by CS.
Cognitive telerehabilitation in mild cognitive impairment, Alzheimer’s disease and frontotemporal dementia: A systematic review
Authors: Cotelli Maria , Manenti Rosa , Brambilla Michela , Gobbi Elena , Ferrari Clarissa , Binetti Giuliano , Cappa Stefano F
Published: November 2017

Introduction

Given the limited effectiveness of pharmacological treatments, non-pharmacological interventions in neurodegenerative diseases have gained increasing attention in recent years and telerehabilitation has been proposed as a cognitive rehabilitation strategy. The purpose of this systematic review is to examine the evidence for the efficacy of cognitive telerehabilitation interventions compared with face-to-face rehabilitation in patients with mild cognitive impairment, Alzheimer’s disease and frontotemporal dementia.

Methods

In accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a systematic search of the Medline database was conducted. Out of 14 articles assessed for eligibility, five studies were identified, three in participants with mild cognitive impairment or Alzheimer’s disease, two in patients with primary progressive aphasia.

Results

The Physiotherapy Evidence Database scale was used to assess the methodological quality of four out of five studies included in this systematic review, with only one report receiving a high-quality rating. Effect-size analysis evidenced positive effects of telerehabilitation interventions, comparable with those reported for face-to-face rehabilitation.

Discussion

The available evidence for the effectiveness of cognitive telerehabilitation is limited, and the quality of the evidence needs to be improved. The systematic review provides preliminary evidence suggesting that cognitive telerehabilitation for neurodegenerative disease may have comparable effects as conventional in-person cognitive rehabilitation.
Evaluating the construct validity of Stress Overload Scale-Short using exploratory structural equation modeling
Authors: Mu Wenlong , Duan Wenjie
Published: November 2017

This study used exploratory structural equation modeling and confirmatory factor analysis to examine the construct validity of the Chinese version of Stress Overload Scale-Short, which included personal vulnerability and event load. The participants included 629 community residents and 495 university students. The results indicated a better goodness-of-fit using exploratory structural equation modeling compared with confirmatory factor analysis. The Stress Overload Scale-Short performed well in distinguishing individuals with more negative emotion symptoms from the general population. A moderation analysis demonstrated that social support moderates the effect of personal vulnerability on negative emotion symptoms. These results facilitated the application of Stress Overload Scale-Short in the current population.
Imaging-Guided Preoperative Localization of Intra-Abdominal Local Recurrences of Colorectal Cancer Using the Harpoon Technique
Authors: Bollo J. , Ferrara F. , Pernas J. C. , Rodriguez-Luppi C. , Targarona E. M. , Trias M.
Published: November 2017

Background and Aims:

Intra-abdominal local recurrences of colorectal cancer can be difficult to localize and excise because they are not easily visible or palpable.

Materials and Methods:

We report on our experience using the computed tomography–guided harpoon technique to locate and resect these nodules in seven patients.

Results:

No complications were recorded during the procedures. Six nodes were malignant and all margins were tumor free.

Conclusions:

Harpoon placement for intra-abdominal local recurrences of colorectal cancer is a feasible and useful technique that provides direct localization and complete excision of lesions.
Comment to ‘Regarding “Diabetes mellitus increases the risk of ruptured abdominal aortic aneurysms”’
Authors: Wierzba Waldemar , Sliwczynski Andrzej , Pinkas Jaroslaw , Jawien Arkadiusz , Karnafel Waldemar
Published: November 2017

This publication is a commentary on the Letter to the Editor by Juliette Raffort and Fabien Lareyre. This article clarifies a number of concerns about the method of calculating the index of prevalence of ruptured abdominal aortic aneurysms (AAA). The method of qualifying patients for the study and the method of calculating the index of prevalence of ruptured AAA in cohorts of diabetic and non-diabetic patients was presented. Most researchers calculate the Index of Prevalence per 100,000 of the general population. This gives the misleading result that diabetes reduces the risk of AAA rupture.We used a method which calculated prevalence per 100,000 with diabetes mellitus and per 100,000 without diabetes mellitus. This method confirms that diabetes mellitus increases the risk of ruptured AAA.
Inflammatory biomarkers and radiologic measurements in never-smokers with COPD: A cross-sectional study from the CODA cohort
Authors: Lee Hyun , Hong Yoonki , Lim Myoung Nam , Bak So Hyeon , Kim Min-Ji , Kim Kyunga , Kim Woo Jin , Park Hye Yun
Published: November 2017

Various biomarkers have emerged as potential surrogates to represent various subgroups of chronic obstructive pulmonary disease (COPD), which manifest with different phenotypes. However, the biomarkers representing never-smokers with COPD have not yet been well elucidated. The aim of this study was to evaluate the associations of certain serum and radiological biomarkers with the presence of COPD in never-smokers. To explore the associations of serum and radiological biomarkers with the presence of COPD in never-smokers, we conducted a cross-sectional patient cohort study composed of never-smokers from the COPD in Dusty Areas (CODA) cohort, consisting of subjects living in dusty areas near cement plants in South Korea. Of the 131 never-smokers in the cohort, 77 (58.8%) had COPD. There were no significant differences in the number of subjects with high levels of inflammatory biomarkers (>90th percentile of never-smokers without COPD), including white blood cell count, total bilirubin, interleukin (IL)-6, IL-8, and C-reactive protein, or radiologic measurements (including emphysema index and mean wall area percentage) between never-smokers with COPD and those without COPD. However, the number of subjects with high uric acid was significantly higher in never-smokers with COPD than never-smokers without COPD (31.2% (24/77) vs. 11.1% (6/54); p = 0.013). In addition, multivariate analysis revealed that high uric acid was significantly associated with the presence of COPD in never-smokers (adjusted relative risk: 1.63; 95% confidence interval: 1.21, 2.18; p = 0.001). Our study suggests that high serum levels of uric acid might be a potential biomarker for assessing the presence of COPD in never-smokers.
Studying the influence of different carbon-fibre-reinforced polymer patches on the mechanical properties of carbon-fibre-reinforced polymer composite
Authors: Weise Daniel , Vorhof Michael , Unger Reimar , Hoffmann Gerald , Cherif Chokri
Published: November 2017

Joining textile layers to a preform using patches is of utter importance in regards to producing structural elements made of fibre-reinforced materials with complex geometry, and repairing fibre-reinforced composites in an efficient and safe manner. Material-efficient and load-specific design and integration of the patch are essential in relation to the performance of the joint as well as the strengthening of the composite structure after a damaging event. Hence, in this study, the stress–strain behaviour of carbon-fibre-reinforced epoxy-composites, which are joined by a patch designed as double-lap joint, will be investigated. It will be shown that the woven fabric morphology (surface structure) and the woven fabric construction (weave pattern) of the join partners exert a noticeable influence on the stability of the patched composite samples. The use of leno non-crimp fabrics as patch structures, which provide an increased joint surface in comparison to the likewise examined twill fabrics, enables a growth in joint strength, provided that the dimensions of the patch remain the same.
A Community-Based Approach to Assessing the Physical, Emotional, and Health Status of Hispanic Breast Cancer Survivors
Authors: Sanchez-Birkhead Ana C. , Carbajal-Salisbury Sara , Larreta Jorge Arce , Lovlien Leslie , Hendricks Hilary , Dingley Catherine , Beck Susan L.
Published: November 2017

Introduction:

Latina breast cancer survivors in the United States face disproportionate risk for poorer quality of life and physical health, as well as greater emotional distress.

Method:

A cross-sectional survey was conducted to describe the physical, emotional, and general health status of 135 Latina breast cancer survivors served by a community-based program.

Results:

Of the 135 surveys sent, 48 survivors responded. Of those who responded, time since diagnosis ranged from 0 to 24 years ( M = 4.37; SD = 5.54); and 45.9% of the women rated physical health as poor or fair. Fatigue prevalence was high, with 60.5% reporting fatigue as moderate or severe. Nearly 80% reported having pain (score >0); 38.3% reported pain was moderate or severe. The women reported mild levels of anxiety and depression but high levels of stress ( M = 4.14; SD = 3.02).

Conclusions:

Latina breast cancer survivors could benefit from interventions focused on commonly shared problems while tailoring specific interventions for subsets with more severe symptoms.
Uncovering How and When Environmental Leadership Affects Employees’ Voluntary Pro-environmental Behavior
Authors: Robertson Jennifer L. , Carleton Erica
Published: November 2017

Environmental sustainability at the firm level is largely shaped by and dependent on individual-level pro-environmental behavior. Accordingly, investigating the antecedents of employees’ environmentally friendly behavior has become the focus of much scholarly inquiry. Research in this area has identified environmentally specific transformational leadership as an important antecedent. Little is known, however, about the mechanisms through which this type of leadership affects employees’ voluntary pro-environmental behavior, and the conditions under which any such effects are enhanced or attenuated. The present research sought to fill this gap. Data from 125 employee dyads revealed that environmentally specific transformational leadership directly and indirectly affects employees’ voluntary pro-environmental behavior, and the indirect effect is only present for employees who are moderate, high, and very high in environmental locus of control. Theoretical and practical implications are discussed.
Factors affecting self-reported medication adherence and hypertension knowledge: A cross-sectional study in rural villages, Yogyakarta Province, Indonesia
Authors: Rahmawati Riana , Bajorek Beata
Published: November 2017

Objectives

This study assessed medication adherence and hypertension knowledge, and their predictive factors, in people with hypertension, living in rural communities in Indonesia.

Methods

Data were acquired from 384 people living in eight rural villages via a researcher-administered questionnaire, a validated adherence scale, and a standardized hypertension knowledge survey. Multivariate analysis was used to identify the predictors of adherence and knowledge.

Results

Fifty-nine (15%) participants had good hypertension knowledge (score ≥ 8 out of 10). Compared to participants with poor knowledge, these participants had higher formal education (odds ratio = 2.7, 95% confidence interval = 1.5–4.7), and lived closer to a community health center (odds ratio = 1.8, 95% confidence interval = 1.0–3.3). Knowledge gaps about the need for long-term medication, hypertension complications, and the target blood pressure were identified. Good hypertension knowledge predicted good adherence to medication (odds ratio = 7.1, 95% confidence interval = 3.3–15.2). Only 42 (11%) participants were considered to have good adherence. Reasons for intentional nonadherence were beliefs that medicines should be taken only when symptoms are evident, limited access to healthcare services, and a preference using traditional medicines.

Conclusion

Strategies for addressing knowledge gaps and misconceptions about hypertension medication are needed, particularly for people with a low educational level and those living some distances from healthcare facilities.
Cerebral amyloid angiopathy, cerebral microbleeds and implications for anticoagulation decisions: The need for a balanced approach
Authors: Charidimou Andreas , Shoamanesh Ashkan , Al-Shahi Salman Rustam , Cordonnier Charlotte , Perry Luke A , Sheth Kevin N , Biffi Alessandro , Rosand Jonathan , Viswanathan Anand
Published: November 2017

Cerebral amyloid angiopathy is a common hemorrhagic small vessel disease of the brain, often associated with high risk of spontaneous lobar intracerebral hemorrhage. When the suspicion of cerebral amyloid angiopathy is raised, clinicians are hesitant in prescribing oral anticoagulation in patients in whom it is otherwise indicated, including the case of non-valvular atrial fibrillation. This is one of the thorniest clinical dilemmas in the field currently. In this short Leading Opinion piece by an international panel of clinicians-researchers active in the field, we present our consistent approach and future outlook on oral anticoagulation post intracerebral hemorrhage and in the setting of clinical-radiologic evidence of cerebral amyloid angiopathy. We discuss recent advances and support a more balanced approach with implications for the wider neurological clinical community in regards to successful recruiting this patient population in ongoing and future randomized trials.
A Cross-Site Analysis of Neotropical Bird Hunting Profiles
Authors: Stafford C. A. , Preziosi R. F. , Sellers W. I.
Published: November 2017

Subsistence hunting of neotropical birds is common and widespread in the tropical forests of Latin America. Although its sustainability under different scenarios is subject to debate, hunting has already contributed to the decline and local extirpation of several taxa and is considered to be a significant threat to a range of large-bodied species. Gaining a better understanding of the variability of hunting patterns, as well as the factors that can potentially be used to predict them, is important if we are to develop conservation strategies that target the species most likely to be experiencing declines. In this article, we examine the avian hunting profiles of 65 communities in the neotropics. We describe their variability and look at the relationship between a hunting profile and (a) its geographical location, (b) the community’s age, (c) the community’s population size, and (d) the year in which the survey was carried out. We find that there is a significant but weak relationship between a community’s geographic location and the composition of its bird hunting profile, and that prey profiles can be considerably different even among close neighbors. We found no relationship between a community’s age or size and the mean biomass of bird prey hunted. Our results challenge the assumption that older and larger settlements have a predictable impact upon avian prey communities and suggest that cultural preferences or the starting availability of prey species can change rapidly over short distances.
“Quality Leadership Matters”: A Research-Based Survey of Graduate Programming
Authors: Mullen Carol A. , Eadens Daniel W.
Published: November 2017

This empirical study contributes to the dialogue about quality leadership and national trends involving standards-based program review. It is the first to utilize the 2016 Council for the Accreditation of Educator Preparation (CAEP) Standards for graduate programs and separately from accreditation and sponsorship. The literature on quality leadership is reviewed, and results from an original instrument are described. Survey influences included leadership literature, the CAEP Standards, and the University Council for Educational Administration’s artifacts. Students and completers’ feedback was on program effectiveness, satisfaction, impact, and ethics. Variance was found in perceptions of quality, relevance, and learning. Contradictory beliefs of program effectiveness can stimulate discussion and strengthen programming.
What are we fighting for? Ideological posturing and anarchist geographies
Authors: Pickerill Jenny
Published: November 2017

Recent debates in radical geography seem determined to be oppositional and in so doing simplify what is at stake. We need to celebrate and maintain the openness of geography to multiple perspectives while simultaneously developing more action-oriented, hopeful ways forward. Anarchist perspectives hold plenty of promise for radical geography, but only if we critically interrogate their principles and empirics.
The role of social anarchism and geography in constructing a radical agenda
Authors: Ackelsberg Martha , Breitbart Myrna Margulies
Published: November 2017

David Harvey’s response to Simon Springer (2014) raises important questions about the places from which to draw ideas for a radical geography agenda. Nevertheless, Harvey ignores critical contributions that social anarchists (including social geographers) have made to understanding both the theory and practice of social transformation. We draw on studies of the anarchist movement in Spain before and during the Spanish Civil War to explore some of what social anarchism has to contribute to geography and contemporary struggles for a more equitable society.
Questioning authority
Authors: Wood Patricia Burke
Published: November 2017

In this commentary, I clarify and expand on anarchists’ positions on order, collectivism, organization, anti-statism, leadership, and the scale of politics. I conclude with some suggestions as to what anarchism has to offer critical geographers.
Unifying by multiplying
Authors: Carolan Michael
Published: November 2017

The author cautions against theories of value that look to define what ‘it’ is, noting how such an approach closes off imaginaries based on alterity and difference thus unintentionally reproducing the very status quo being criticizing. A call is made for experimentation, disciplinary transgressions, and cosmopolitical critiques. Can we think about theories of value that are critical and hopeful?
From value as theoretical object to rent as political project
Authors: Lewis Nick
Published: November 2017

Directing attention to ‘value’ and ‘valuing’ as objects of scholarly research offers a promising platform for building a new politics of geography and of livelihoods in relation to economic activities involving the commons, nonhuman species, and environmental resources. This paper responds to Kay and Kenny-Lazar’s survey of recent debates in this regard. It makes the claim that while refocusing scholarship on the materiality of value is a welcome intervention, the challenge is to covert this attention to a new politics in the world by escaping the narrow theoretical language and framings they deploy. I refer to my own work in Aotearoa New Zealand to suggest that this may be achieved in part by extending ‘value thinking’ to ‘rent thinking’ and mobilizing both sets of ideas in enactive, applied research.
Valuing nature within and beyond capitalism
Authors: Kenney-Lazar Miles , Kay Kelly
Published: November 2017

This paper is a response to commentaries on our article entitled ‘Value in capitalist natures: an emerging framework’ (Kay and Kenney-Lazar, 2017). We argue that the responses to our initial paper served to broaden our proposed framework and to underscore the need for a unified, but diverse, approach to nature–society studies with value at its center. Extending the argument from the initial article, we continue to see potential for value to act as a bridge that can bring together diverse scholarship in nature–society geography and political ecology. After briefly addressing both the tensions and possibilities for value as a bridging concept, we focus our response primarily around three major threads that emerged across the commentaries. First, we address points raised by the respondents concerning the bounding of capitalism and its permeation into socionatures. Second, we engage with value’s inverse and its absence, captured through the concepts of ‘devaluation’ (Collard and Dempsey) and ‘disvalues’ (Sullivan). Finally, we close by engaging the possibility of a ‘liberatory valuing of nature’—one which recognizes a multiplicity of social and ecological values as a means of working toward more just and emancipatory nature–society relations beyond capitalism.
50 years of the Declaration on Christian Education Gravissimum Educationis: A review of its reception in Latin America
Authors: Madero Cristóbal
Published: November 2017

This article presents an historical and critical review of the Declaration on Christian Education Gravissimum Educationis, promulgated on October 28, 1965, during the fourth and last session of Vatican II. By considering the history and context of this document, and after evaluating the three socio-ecclesial factors that were behind the text, an assessment of the reception of Gravissimum Educationis principles in the Latin American Church is made. The Conference of Bishops at Medellín in 1968 rejected many points of Gravissimum Educationis. In 1979, the Third General Conference at Puebla proposed a new concept of education for the continent. The bishops considered that education has to be, first of all, an evangelizing task. By analyzing the state of education in the continent, the Fifth Conference at Aparecida also criticizes trends that impoverished the real purpose of education in the continent. The article concludes that both the content and the history behind Gravissimum Educationis make this declaration of Vatican II a lesser document in comparison to other conciliar documents such as Gaudium et spes or Lumen gentium. Even though the Declaration introduces some principles of education and schooling, these are presented in a defensive form, precisely a form that other main conciliar documents try to avoid. For these reasons, Gravissimum Educationis was not well-received in Latin America.
Exploring the professional ideals of Christian teachers from conservative Protestant schools in the Netherlands
Authors: Boele-de Bruin HL (Laura) , de Muynck A (Bram)
Published: November 2017

Professional ideals arise from personal worldviews and specify teachers' professional identities. This study aimed to explore how faith is present in the professional ideals of Christian teachers. The professional ideals of 107 Dutch teachers from conservative Protestant primary and secondary schools were explored using an open-ended questionnaire. The ideal educational aims and contents were closely connected: the ultimate essence of teaching was defined as passing on images of the perfect Christian person by modelling. Faith was represented by non-substantial religious ideals that are related to social behavior. Ideals about didactical strategies and teaching materials which demonstrate teachers' Christian worldview were hardly found.
Evaluating Effective Leadership and Governance in a Midwestern Agricultural Safety and Health Coalition
Authors: Wendl Mary J. , Cramer Mary E.
Published: November 2017

Agricultural Centers are a coalition of organizations and individual members with a common purpose: to improve the health and safety of the agricultural community. Successful leadership and governance are essential in accomplishing these goals. This article examined the effectiveness of a midwestern Agricultural Health and Safety Center (Ag Center) leadership and governance structure. The Internal Coalition Outcomes Hierarchy (ICOH) framework and the Internal Coalition Effectiveness (ICE©) instrument were used, with field visit interviews conducted to gain further insight. Combined comparative findings from both research methods showed that scores in each of the categories increased. Adjustments led to stronger collaborative leadership, vital to successful population health improvement programs. This study showcases coalition qualities in a broader environment, capturing a clearer depiction of leadership and member interaction. Field visit interviews confirmed that this midwestern Ag Center continued to have strong levels of effectiveness in each of the conceptual constructs of a coalition.
Early-Life Pseudomonas aeruginosa Infection in Cystic Fibrosis and Lung Disease Progression
Authors: Petrocheilou Argyri , Papagrigoriou-Theodoridou Maria , Michos Athanasios , Doudounakis Stavros-Eleftherios , Loukou Ioanna , Kaditis Athanasios
Published: November 2017

Lung disease in cystic fibrosis (CF) starts early, with studies identifying abnormalities on chest computed tomography (CT) scan even in infancy. In this retrospective study, abnormal chest CT was the main outcome; body mass index (BMI) z score and forced expiratory volume percent predicted (FEV1%) predicted at age 6 to 7 years were secondary outcomes. Pseudomonas aeruginosa infection prior to 12 months of age was the main explanatory variable. There was no association between early P aeruginosa infection and abnormal CT after adjustment for CFTR (cystic fibrosis transmembrane conductance regulator) functional mutation class, gender, and other pathogens (odds ratio = 0.30; 95% confidence interval = 0.07-1.35; P = .11). No significant associations were demonstrated for BMI z score and FEV1% predicted. Children with class I-III CFTR mutations had increased risk of abnormal CT findings (odds ratio = 11.67; 95% confidence interval = 1.11-115.06; P = .035) and lower FEV1% predicted ( P = .04). In the current era, early-life P aeruginosa infection in CF might not influence the severity of lung disease in school age as much as previously. Larger studies are needed to confirm this finding.