bluuebunny/crossref_metadata_2025 huggingface dataset:
Doublecortin marks a new population of transiently amplifying muscle progenitor cells and is required for myofiber maturation during skeletal muscle regeneration
Authors: Ogawa Ryo , Ma Yuran , Yamaguchi Masahiko , Ito Takahito , Watanabe Yoko , Ohtani Takuji , Murakami Satoshi , Uchida Shizuka , De Gaspari Piera , Uezumi Akiyoshi , Nakamura Miki , Miyagoe-Suzuki Yuko , Tsujikawa Kazutake , Hashimoto Naohiro , Braun Thomas , Tanaka Teruyuki , Takeda Shin'ichi , Yamamoto Hiroshi , Fukada So-ichiro
Published: December 2014

Muscle satellite cells are indispensable for muscle regeneration, but the functional diversity of their daughter cells is unknown. Here, we show that many Pax7+MyoD− cells locate both beneath and outside the basal lamina during myofiber maturation. A large majority of these Pax7+MyoD− cells are not self-renewed satellite cells, but have different potentials for both proliferation and differentiation from Pax7+MyoD+ myoblasts (classical daughter cells), and are specifically marked by expression of the doublecortin (Dcx) gene. Transplantation and lineage-tracing experiments demonstrated that Dcx-expressing cells originate from quiescent satellite cells and that the microenvironment induces Dcx in myoblasts. Expression of Dcx seems to be necessary for myofiber maturation because Dcx-deficient mice exhibited impaired myofiber maturation resulting from a decrease in the number of myonuclei. Furthermore, in vitro and in vivo studies suggest that one function of Dcx in myogenic cells is acceleration of cell motility. These results indicate that Dcx is a new marker for the Pax7+MyoD− subpopulation, which contributes to myofiber maturation during muscle regeneration.
Coordinate control of terminal dendrite patterning and dynamics by the membrane protein Raw
Authors: Lee Jiae , Peng Yun , Lin Wen-Yang , Parrish Jay Z.
Published: December 2014

The directional flow of information in neurons depends on compartmentalization: dendrites receive inputs whereas axons transmit them. Axons and dendrites likewise contain structurally and functionally distinct subcompartments. Axon/dendrite compartmentalization can be attributed to neuronal polarization, but the developmental origin of subcompartments in axons and dendrites is less well understood. To identify the developmental bases for compartment-specific patterning in dendrites, we screened for mutations that affect discrete dendritic domains in Drosophila sensory neurons. From this screen, we identified mutations that affected distinct aspects of terminal dendrite development with little or no effect on major dendrite patterning. Mutation of one gene, raw, affected multiple aspects of terminal dendrite patterning, suggesting that Raw might coordinate multiple signaling pathways to shape terminal dendrite growth. Consistent with this notion, Raw localizes to branch-points and promotes dendrite stabilization together with the Tricornered (Trc) kinase via effects on cell adhesion. Raw independently influences terminal dendrite elongation through a mechanism that involves modulation of the cytoskeleton, and this pathway is likely to involve the RNA-binding protein Argonaute 1 (AGO1), as raw and AGO1 genetically interact to promote terminal dendrite growth but not adhesion. Thus, Raw defines a potential point of convergence in distinct pathways shaping terminal dendrite patterning.
Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast
Authors: Guzman-Ayala Marcela , Sachs Michael , Koh Fong Ming , Onodera Courtney , Bulut-Karslioglu Aydan , Lin Chih-Jen , Wong Priscilla , Nitta Rachel , Song Jun S. , Ramalho-Santos Miguel
Published: December 2014

The pluripotent mammalian epiblast undergoes unusually fast cell proliferation. This rapid growth is expected to generate a high transcriptional demand, but the underlying mechanisms remain unknown. We show here that the chromatin remodeler Chd1 is required for transcriptional output and development of the mouse epiblast. Chd1−/− embryos exhibit proliferation defects and increased apoptosis, are smaller than controls by E5.5 and fail to grow, to become patterned or to gastrulate. Removal of p53 allows progression of Chd1−/− mutants only to E7.0-8.0, highlighting the crucial requirement for Chd1 during early post-implantation development. Chd1−/− embryonic stem cells (ESCs) have a self-renewal defect and a genome-wide reduction in transcriptional output at both known mRNAs and intergenic transcripts. These transcriptional defects were only uncovered when cell number-normalized approaches were used, and correlate with a lower engagement of RNAP II with transcribed genes in Chd1−/− ESCs. We further show that Chd1 directly binds to ribosomal DNA, and that both Chd1−/− epiblast cells in vivo and ESCs in vitro express significantly lower levels of ribosomal RNA. In agreement with these findings, mutant cells in vivo and in vitro exhibit smaller and more elongated nucleoli. Thus, the RNA output by both Pol I and II is reduced in Chd1−/− cells. Our data indicate that Chd1 promotes a globally elevated transcriptional output required to sustain the distinctly rapid growth of the mouse epiblast.
The centrosome orientation checkpoint is germline stem cell specific and operates prior to the spindle assembly checkpoint in Drosophila testis
Authors: Venkei Zsolt G. , Yamashita Yukiko M.
Published: December 2014

Asymmetric cell division is utilized by a broad range of cell types to generate two daughter cells with distinct cell fates. In stem cell populations asymmetric cell division is believed to be crucial for maintaining tissue homeostasis, failure of which can lead to tissue degeneration or hyperplasia/tumorigenesis. Asymmetric cell divisions also underlie cell fate diversification during development. Accordingly, the mechanisms by which asymmetric cell division is achieved have been extensively studied, although the check points that are in place to protect against potential perturbation of the process are poorly understood. Drosophila melanogaster male germline stem cells (GSCs) possess a checkpoint, termed the centrosome orientation checkpoint (COC), that monitors correct centrosome orientation with respect to the component cells of the niche to ensure asymmetric stem cell division. To our knowledge, the COC is the only checkpoint mechanism identified to date that specializes in monitoring the orientation of cell division in multicellular organisms. Here, by establishing colcemid-induced microtubule depolymerization as a sensitive assay, we examined the characteristics of COC activity and find that it functions uniquely in GSCs but not in their differentiating progeny. We show that the COC operates in the G2 phase of the cell cycle, independently of the spindle assembly checkpoint. This study may provide a framework for identifying and understanding similar mechanisms that might be in place in other asymmetrically dividing cell types.
Stress-induced endogenous siRNAs targeting regulatory intron sequences in Brachypodium
Authors: Wang Hsiao-Lin V. , Dinwiddie Brandon L. , Lee Herman , Chekanova Julia A.
Published: December 2014

Exposure to abiotic stresses triggers global changes in the expression of thousands of eukaryotic genes at the transcriptional and post-transcriptional levels. Small RNA (smRNA) pathways and splicing both function as crucial mechanisms regulating stress-responsive gene expression. However, examples of smRNAs regulating gene expression remain largely limited to effects on mRNA stability, translation, and epigenetic regulation. Also, our understanding of the networks controlling plant gene expression in response to environmental changes, and examples of these regulatory pathways intersecting, remains limited. Here, to investigate the role of smRNAs in stress responses we examined smRNA transcriptomes of Brachypodium distachyon plants subjected to various abiotic stresses. We found that exposure to different abiotic stresses specifically induced a group of novel, endogenous small interfering RNAs (stress-induced, UTR-derived siRNAs, or sutr-siRNAs) that originate from the 3′ UTRs of a subset of coding genes. Our bioinformatics analyses predicted that sutr-siRNAs have potential regulatory functions and that over 90% of sutr-siRNAs target intronic regions of many mRNAs in trans. Importantly, a subgroup of these sutr-siRNAs target the important intron regulatory regions, such as branch point sequences, that could affect splicing. Our study indicates that in Brachypodium, sutr-siRNAs may affect splicing by masking or changing accessibility of specific cis-elements through base-pairing interactions to mediate gene expression in response to stresses. We hypothesize that this mode of regulation of gene expression may also serve as a general mechanism for regulation of gene expression in plants and potentially in other eukaryotes.
Identification of 5-Bromo-2’-Deoxyuridine-Labeled Cells during Mouse Spermatogenesis by Heat-Induced Antigen Retrieval in Lectin Staining and Immunohistochemistry
Authors: Wakayama Tomohiko , Nakata Hiroki , Kumchantuek Tewarat , Gewaily Mahmoud Saad , Iseki Shoichi
Published: December 2014

DNA replication occurs during S-phase in spermatogonia and preleptotene spermatocytes during spermatogenesis. 5-Bromo-2’-deoxyuridine (BrdU) is incorporated into synthesized DNA and is detectable in the nucleus by immunohistochemistry (IHC). To identify BrdU-labeled spermatogenic cells, the spermatogenic stages must be determined by visualizing acrosomes and detecting cell type-specific marker molecules in the seminiferous tubules. However, the antibody reaction with BrdU routinely requires denaturation of the DNA, which is achieved by pretreating tissue sections with hydrochloric acid; however, this commonly interferes with further histochemical approaches. Therefore, we examined optimal methods for pretreating paraffin sections of the mouse testis to detect incorporated BrdU by an antibody and, at the same time, visualize acrosomes with peanut agglutinin (PNA) or detect several marker molecules with antibodies. We found that the use of heat-induced antigen retrieval (HIAR), which consisted of heating at 95C in 20 mM Tris-HCl buffer (pH 9.0) for 15 min, was superior to the use of 2 N hydrochloric acid for 90 min at room temperature in terms of the quality of subsequent PNA-lectin histochemistry with double IHC for BrdU and an appropriate stage marker protein. With this method, we identified BrdU-labeled spermatogenic cells during mouse spermatogenesis as A1 spermatogonia through to preleptotene spermatocytes.
Identical Expression Profiling of Human and Murine TIPE3 Protein Reveals Links to Its Functions
Authors: Cui Jian , Hao Chunyan , Zhang Wenqian , Shao Jie , Zhang Na , Zhang Guizhong , Liu Suxia
Published: December 2014

Tumor necrosis factor-alpha-induced protein-8 like-3 (TNFAIP8L3, TIPE3) is a newly discovered member of TNFAIP8 family and regarded as a lipid second messenger transfer protein that promotes cancer. Yet the nature of the cells and tissues that express TIPE3 protein has not been determined. In this study, we examined TIPE3 expression in various murine and human tissues by immunohistochemistry and quantitative PCR. We found that TIPE3 expression was almost identical in most organs from human and mice. TIPE3 is a cytoplasmic protein expressed preferentially in epithelial-derived cells with secretory functions. Furthermore, TIPE3 protein is highly expressed in most human carcinoma cell lines. These results suggest that TIPE3 may play important roles in carcinogenesis and cell secretion.
Towards a methodology for measuring media plurality
Authors: Elstein David
Published: December 2014

The central objective in addressing media plurality is to ensure that no single body or person exercises an undue degree of influence over the flow of information and the formation of political opinion in the United Kingdom. David Elstein examines the media market in the United Kingdom and finds it lacks plurality and diversity since it is dominated by one actor, namely the BBC (British Broadcasting Corporation).
Small colony variant of Escherichia coli isolated from a recurrent urinary tract infection- a case report
Authors: Dutt Shivendra , N Nagalakshmi , K.L Shobha
Published: December 2014

Introduction: Small colony variant of Escherichia coli may cause persistent and recurrent infections in human. These slow growing phenotypic variants are difficult to identify and mislead the diagnosis which can lead to choice of inappropriate antibiotics. In this case report we are presenting a case of recurrent urinary tract infection which was associated with small colony variants of E. coli.Case presentation: A two year old male child was admitted to the hospital with a complaint of passing thin stream of urine. One month earlier the child had been previously diagnosed with bilateral grade five Vesicoureteral reflux. Child had developed recurrent urinary tract infection caused by small colony variants of E. coli.Conclusion: child had undergone bilateral ureter reimplantation as part of treatment to Vesicoureteral reflux. Since vesicoureteral reflex condition is one of the risk factor to develop urinary tract infections. Repeated exposure to antibiotic might have been induced stress condition to bacteria and emerged as slow growing sub population of E. coli.
Fuzzy spanners
Authors: Farshi Mohammad
Published: December 2014

Graphs have wide applications in variety of applications, especially network analysis. Spanners give a sparse approximation of any graph as well as complete graph, which has wide applications so far. Because of its applications, graph definitions generalized to fuzzy sets and fuzzy weighted graph defined and studied vastly in past and has applications in several fields. In this paper, we define spanners for fuzzy weighted graphs and well as points come from a fuzzy metric space. We propose some algorithm to compute such a spanner. Finally, we pose some open problem that can be considered for future works.
IT Governance Awareness and Practices: an Insight from Malaysian Senior Management Perspective
Authors: Lin Yap May , Arshad Noor Habibah , Haron Halilah , Wah Yap Bee , Yusoff Muhammad , Mohamed Azlinah
Published: December 2014

While corporate governance is now receiving due attention in the Asian region, IT governance (ITG) does not appear to be given much credence even though business processes today mandate IT. It is observed that awareness and practices of ITG do not seem to be widespread in the region. Using senior management sample data from Malaysian organizations, a study was conducted to determine the awareness and practices of ITG. Contrary to observation, findings indicated that Malaysian businesses appeared to exhibit awareness but ITG was only partially practiced. There was positive correlation between both concepts. Although the association was not causal, it revealed the potential tendency for awareness to cascade down to practices in an operating environment. ITG practices may be strengthened through senior management commitment and involvement, oversight committees, and real-world issues experienced by organizations such as the focus on IT creating tangible value to real stakeholders and the strategic alignment of IT to include the real business environment.
A Major Controversy in Codon-Anticodon Adaptation Resolved by a New Codon Usage Index
Authors: Xia Xuhua
Published: December 2014

Two alternative hypotheses attribute different benefits to codon-anticodon adaptation. The first assumes that protein production is rate limited by both initiation and elongation and that codon-anticodon adaptation would result in higher elongation efficiency and more efficient and accurate protein production, especially for highly expressed genes. The second claims that protein production is rate limited only by initiation efficiency but that improved codon adaptation and, consequently, increased elongation efficiency have the benefit of increasing ribosomal availability for global translation. To test these hypotheses, a recent study engineered a synthetic library of 154 genes, all encoding the same protein but differing in degrees of codon adaptation, to quantify the effect of differential codon adaptation on protein production in Escherichia coli. The surprising conclusion that “codon bias did not correlate with gene expression” and that “translation initiation, not elongation, is rate-limiting for gene expression” contradicts the conclusion reached by many other empirical studies. In this paper, I resolve the contradiction by reanalyzing the data from the 154 sequences. I demonstrate that translation elongation accounts for about 17% of total variation in protein production and that the previous conclusion is due to the use of a codon adaptation index (CAI) that does not account for the mutation bias in characterizing codon adaptation. The effect of translation elongation becomes undetectable only when translation initiation is unrealistically slow. A new index of translation elongation ITE is formulated to facilitate studies on the efficiency and evolution of the translation machinery.
Evidence for Emergence of Sex-Determining Gene(s) in a Centromeric Region in Vasconcellea parviflora
Authors: Iovene Marina , Yu Qingyi , Ming Ray , Jiang Jiming
Published: December 2014

Sex chromosomes have been studied in many plant and animal species. However, few species are suitable as models to study the evolutionary histories of sex chromosomes. We previously demonstrated that papaya (Carica papaya) (2n = 2x = 18), a fruit tree in the family Caricaceae, contains recently emerged but cytologically heteromorphic X/Y chromosomes. We have been intrigued by the possible presence and evolution of sex chromosomes in other dioecious Caricaceae species. We selected a set of 22 bacterial artificial chromosome (BAC) clones that are distributed along the papaya X/Y chromosomes. These BACs were mapped to the meiotic pachytene chromosomes of Vasconcellea parviflora (2n = 2x = 18), a species that diverged from papaya ∼27 million years ago. We demonstrate that V. parviflora contains a pair of heteromorphic X/Y chromosomes that are homologous to the papaya X/Y chromosomes. The comparative mapping results revealed that the male-specific regions of the Y chromosomes (MSYs) probably initiated near the centromere of the Y chromosomes in both species. The two MSYs, however, shared only a small chromosomal domain near the centromere in otherwise rearranged chromosomes. The V. parviflora MSY expanded toward the short arm of the chromosome, whereas the papaya MSY expanded in the opposite direction. Most BACs mapped to papaya MSY were not located in V. parviflora MSY, revealing different DNA compositions in the two MSYs. These results suggest that mutation of gene(s) in the centromeric region may have triggered sex chromosome evolution in these plant species.
Oncogenic Alterations in ERBB2/HER2 Represent Potential Therapeutic Targets Across Tumors From Diverse Anatomic Sites of Origin
Authors: Chmielecki Juliann , Ross Jeffrey S. , Wang Kai , Frampton Garrett M. , Palmer Gary A. , Ali Siraj M. , Palma Norma , Morosini Deborah , Miller Vincent A. , Yelensky Roman , Lipson Doron , Stephens Philip J.
Published: December 2014

Background.

Targeted ERBB2/HER2 inhibitors are approved by the U.S. Food and Drug Administration for the treatment of breast, gastric, and esophageal cancers that overexpress or amplify HER2/ERBB2, as measured by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), respectively. Activating mutations in ERBB2 have also been reported and are predicted to confer sensitivity to these targeted agents. Testing for these mutations is not performed routinely, and FISH and IHC are not applied outside of these approved indications.

Materials and Methods.

We explored the spectrum of activating ERBB2 alterations across a collection of ∼7,300 solid tumor specimens that underwent comprehensive genomic profiling using next-generation sequencing. Results were analyzed for base substitutions, insertions and deletions, select rearrangements, and copy number changes.

Results.

Known oncogenic ERBB2 alterations were identified in tumors derived from 27 tissues, and ERBB2 amplification in breast, gastric, and gastroesophageal cancers accounted for only 30% of these alterations. Activating mutations in ERBB2 were identified in 131 samples (32.5%); amplification was observed in 246 samples (61%). Two samples (0.5%) harbored an ERBB2 rearrangement. Ten samples (2.5%) harbored multiple ERBB2 mutations, yet mutations and amplifications were mutually exclusive in 91% of mutated cases.

Conclusion.

Standard slide-based tests for overexpression or amplification of ERBB2 would fail to detect the majority of activating mutations that occur overwhelmingly in the absence of copy number changes. Compared with current clinical standards, comprehensive genomic profiling of a more diverse set of tumor types may identify ∼3.5 times the number of patients who may benefit from ERBB2-targeted therapy.
Integration of Oncology and Palliative Care: A Systematic Review
Authors: Hui David , Kim Yu Jung , Park Ji Chan , Zhang Yi , Strasser Florian , Cherny Nathan , Kaasa Stein , Davis Mellar P. , Bruera Eduardo
Published: December 2014

Background.

Both the American Society of Clinical Oncology and the European Society for Medical Oncology strongly endorse integrating oncology and palliative care (PC); however, a global consensus on what constitutes integration is currently lacking. To better understand what integration entails, we conducted a systematic review to identify articles addressing the clinical, educational, research, and administrative indicators of integration.

Materials and Methods.

We searched Ovid MEDLINE and Ovid EMBase between 1948 and 2013. Two researchers independently reviewed each citation for inclusion and extracted the indicators related to integration. The inter-rater agreement was high (κ = 0.96, p < .001).

Results.

Of the 431 publications in our initial search, 101 were included. A majority were review articles (58%) published in oncology journals (59%) and in or after 2010 (64%, p < .001). A total of 55 articles (54%), 33 articles (32%), 24 articles (24%), and 14 articles (14%) discussed the role of outpatient clinics, community-based care, PC units, and inpatient consultation teams in integration, respectively. Process indicators of integration include interdisciplinary PC teams (n = 72), simultaneous care approach (n = 71), routine symptom screening (n = 25), PC guidelines (n = 33), care pathways (n = 11), and combined tumor boards (n = 10). A total of 66 articles (65%) mentioned early involvement of PC, 18 (18%) provided a specific timing, and 28 (28%) discussed referral criteria. A total of 45 articles (45%), 20 articles (20%), and 66 articles (65%) discussed 8, 4, and 9 indicators related to the educational, research, and administrative aspects of integration, respectively.

Conclusion.

Integration was a heterogeneously defined concept. Our systematic review highlighted 38 clinical, educational, research, and administrative indicators. With further refinement, these indicators may facilitate assessment of the level of integration of oncology and PC.
Simplified finite-element modelling for tunnelling-induced settlements
Authors: Likitlersuang Suched , Surarak Chanaton , Suwansawat Suchatvee , Wanatowski Dariusz , Oh Erwin , Balasubramaniam Arumugam
Published: December 2014

Tunnelling-induced ground surface settlement prediction still adopts empirical and analytical approaches; thus a step further in using a practical numerical analysis is now a challenging task. Because the deformation during tunnelling is a three-dimensional problem, several features were incorporated in two-dimensional analyses to capture aspects that are important in governing behaviour in the missing third dimension. This paper aims to present simplified methods for ground settlement computation of tunnelling works using the PLAXIS finite-element programme. Three simplified methods – contraction ratio, stress reduction and modified grout pressure – were considered in this study. Practical application requires correlations among these three methods. Such correlations among the three methods are proposed in this study and can be used in geotechnical practice. The results were based on a series of finite-element analyses of the Blue Line Bangkok Mass Rapid Transit tunnels. The geotechnical parameters were selected based on soil investigation reports carried out for construction purposes. The soil constitutive model adopted herein was the hardening soil model on soft and stiff clays. All the finite-element simulations were compared with the measured field deformations. Therefore, the analysis results can be considered as a Class-C prediction (back-analysis).
Briefing: Affirming alliancing procurement for Christchurch rebuild, New Zealand
Authors: Le Masurier Jason
Published: December 2014

Following £20 billion of earthquake damage in 2010 and 2011, rebuilding of roads, water and wastewater infrastructure in Christchurch, New Zealand, is being carried out by an alliance called the Stronger Christchurch Infrastructure Rebuild Team (Scirt). This paper aims to demonstrate that alliancing, as an unconventional procurement option locally, provides the best value and possibly the only feasible solution, given the local market conditions.
The performance of place
Authors: Bentley Ian , Kiddle Rebecca
Published: December 2014

This paper argues that urban designers need a new conception of art if they are to create lovable places that respond adequately to ‘big’ social, economic and environmental issues. The paper acknowledges the need to think about settlements as complex systems made up of a number of subsystems. Designers consider both the individual subsystems on their own in addition to analysing the relationships between these different subsystems, thus setting up a ‘central memory archive’. This archive details positive types or minimum specifications from which to create the art of urban design, an analogy being that of performance art: dynamic, multisensory and created through collaboration between expert users and designers.
Community and streetscapes: the art of urban design revisited
Authors: Guise Richard
Published: December 2014

Camillo Sitte argued that town planning should incorporate artistic principles. Raymond Unwin, Gordon Cullen, Kevin Lynch and many others have developed this theme, demonstrating how urban form can be artfully manipulated, to be attractive and stimulating, producing distinctive townscapes rich in texture and meaning. However, this approach has often been criticised as being merely picturesque and subjective. This paper discusses the considerable agenda underpinning the artistic approach (rather than public art) and mainly draws on UK experience, up to the present day. It will argue that – far from being an irrelevant sideline – this approach has, while addressing the Vitruvian ideals of beauty and delight, incorporated practical solutions to many contemporary urban design issues: traffic-calmed streets, mixed uses and placemaking. With the debate in the UK about the re-evaluation of the garden city concept to address the massive shortfall in housing construction and the aim to incorporate ‘wellbeing’ within urban design, is it time to identify and distil those principles of the artistic approach to enrich urban design education and inform policy and practice?
Briefing: Design and the lost art of urbanism
Authors: Falk Nicholas
Published: December 2014

In his final book Sir Peter Hall, with the author's help, chose some 20 European cities to explain how the UK (and USA) could transform their situation by applying the ‘art of urbanism’. German cities best show how to boost the local economy, French cities transport, Dutch cities housing and Scandinavian cities the environment. However, all share a common approach in which local authorities lead the way, and use good urban design to reshape their urban areas, and create better lives for their residents.
Pattern recognition in long‐term Sooty Shearwater data: applying machine learning to create a harvest index
Authors: Humphries G. R. W. , Bragg C. , Overton J. , Lyver P. O'B. , Moller H.
Published: December 2014

Rakiura Māori (New Zealand's southernmost group of indigenous peoples) have harvested the chicks of burrow‐nesting Sooty Shearwaters (Tītī; Puffinus griseus) for generations. As part of the harvest process, some families have maintained annual harvest diaries, some dating back to the 1950s. We used generalized boosted regression models, a machine‐learning algorithm, to calculate a harvest index that takes into account factors that could impact the numbers of birds taken on any given hunt. For predicted vs. observed values, r2 was between 0.59 and 0.90 for the nanao (first half of the season, when chicks are harvested from burrows during the day) and 0.67 and 0.88 for the rama (second half of the season, during which chicks are harvested from the surface at night). Exploration of the controlling factors of the models revealed that “day of season” plays an important role in predicting daily harvest during the second half of the season (the rama). The nightly tally in the rama peaked approximately halfway through (10–15 days in), which is probably related to the timing of birds emerging from burrows to fledge. The models also suggested that data from the rama (when chicks are 100–120 days old) may be the most suitable for long‐term monitoring of populations of Sooty Shearwaters due to consistencies in calculated harvest indices between diaries. Nanao harvest indices, although less consistent, showed patterns similar to those of the rama. When comparing these data to the harvest indices calculated by general linear models by Clucas and colleagues, we found that the agreement between both indices was r2 = 0.31 and r2 = 0.59 for the nanao and rama, respectively. The use of machine learning to correct for extraneous factors (e.g., hunting effort, skill level, or weather) and to create standardized measures could be applied to other systems such as fisheries or terrestrial resource management.
Having our yards and sharing them too: the collective effects of yards on native bird species in an urban landscape
Authors: Belaire J. Amy , Whelan Christopher J. , Minor Emily S.
Published: December 2014

Residential yards comprise a substantial portion of urban landscapes, and the collective effects of the management of many individual yards may “scale up” to affect urban biodiversity. We conducted bird surveys and social surveys in Chicago‐area (Illinois, USA) residential neighborhoods to identify the relative importance of yard design and management activities for native birds. We found that groups of neighboring yards, in the aggregate, were more important for native bird species richness than environmental characteristics at the neighborhood or landscape scale. The ratio of evergreen to deciduous trees in yards and the percentage of yards with trees and plants with fruits or berries were positively associated with native bird species richness, whereas the number of outdoor cats had a negative association. The number of birdfeeders was not an important predictor for native species richness. We also found that migratory birds were observed on transects with more wildlife‐friendly features in yards, and nonnative birds were observed on transects with greater numbers of outdoor cats and dogs. Our results highlight the potential importance of residential matrix management as a conservation strategy in urban areas.
Selective‐logging and oil palm: multitaxon impacts, biodiversity indicators, and trade‐offs for conservation planning
Authors: Edwards David P. , Magrach Ainhoa , Woodcock Paul , Ji Yinqiu , Lim Norman T.-L. , Edwards Felicity A. , Larsen Trond H. , Hsu Wayne W. , Benedick Suzan , Khen Chey Vun , Chung Arthur Y. C. , Reynolds Glen , Fisher Brendan , Laurance William F. , Wilcove David S. , Hamer Keith C. , Yu Douglas W.
Published: December 2014

Strong global demand for tropical timber and agricultural products has driven large‐scale logging and subsequent conversion of tropical forests. Given that the majority of tropical landscapes have been or will likely be logged, the protection of biodiversity within tropical forests thus depends on whether species can persist in these economically exploited lands, and if species cannot persist, whether we can protect enough primary forest from logging and conversion. However, our knowledge of the impact of logging and conversion on biodiversity is limited to a few taxa, often sampled in different locations with complex land‐use histories, hampering attempts to plan cost‐effective conservation strategies and to draw conclusions across taxa. Spanning a land‐use gradient of primary forest, once‐ and twice‐logged forests, and oil palm plantations, we used traditional sampling and DNA metabarcoding to compile an extensive data set in Sabah, Malaysian Borneo for nine vertebrate and invertebrate taxa to quantify the biological impacts of logging and oil palm, develop cost‐effective methods of protecting biodiversity, and examine whether there is congruence in response among taxa. Logged forests retained high species richness, including, on average, 70% of species found in primary forest. In contrast, conversion to oil palm dramatically reduces species richness, with significantly fewer primary‐forest species than found on logged forest transects for seven taxa. Using a systematic conservation planning analysis, we show that efficient protection of primary‐forest species is achieved with land portfolios that include a large proportion of logged‐forest plots. Protecting logged forests is thus a cost‐effective method of protecting an ecologically and taxonomically diverse range of species, particularly when conservation budgets are limited. Six indicator groups (birds, leaf‐litter ants, beetles, aerial hymenopterans, flies, and true bugs) proved to be consistently good predictors of the response of the other taxa to logging and oil palm. Our results confidently establish the high conservation value of logged forests and the low value of oil palm. Cross‐taxon congruence in responses to disturbance also suggests that the practice of focusing on key indicator taxa yields important information of general biodiversity in studies of logging and oil palm.
Long‐term monitoring reveals differing impacts of elephants on elements of a canopy shrub community
Authors: Landman Marietjie , Schoeman David S. , Hall-Martin Anthony J. , Kerley Graham I. H.
Published: December 2014

The conservation management of southern Africa's elephants focuses on identifying and mitigating the extent and intensity of impacts on biological diversity. However, variation in the intensity of elephant effects between elements of biodiversity is seldom explored, which limits our ability to interpret the scale of the impacts. Our study quantifies >50 years of impacts in the succulent thickets of the Addo Elephant National Park, South Africa, contrasting hypotheses for the resilience of the canopy shrubs (a key functional guild) to elephants with those that argue the opposite. We also assess the impacts between elements of the community, ranging from community composition and structure to the structure of individual canopy species. We show the vulnerability of the canopy shrubs to transformation as the accumulated influences of elephants alter community composition and structure. The pattern of transformation is similar to that caused by domestic herbivores, which leads us to predict that elephants will eventually bring about landscape‐level degradation and a significant loss of biodiversity. While we expected the canopy species to show similar declining trends in structure, providing insight into the response of the community as a whole, we demonstrate an uneven distribution of impacts between constituent elements; most of the canopy dominants exhibited little change, resisting removal. This implies that these canopy dominants might not be useful indicators of community change in thickets, a pattern that is likely repeated among the canopy trees of savanna systems. Our findings suggest that predicting elephant impacts, and finding solutions to the so‐called “elephant problem,” require a broader and more integrated understanding of the mechanisms driving the changes between elements of biodiversity at various spatial and temporal scales.
Pig Slurry Residual Effects on Maize Yields and Nitrate Leaching: A Study in Lysimeters
Authors: Yagüe M. R. , Quílez D.
Published: December 2014

Pig (Sus scrofa domesticus) slurry (PS) is often applied year after year to the same fields, and its residual effects under Mediterranean conditions are not well understood. This study assessed the residual effects of PS combined with inorganic N fertilizer, on irrigated monoculture maize (Zea maysL.) yields and nitrate leaching. Grain yield and nitrate leaching in the fifth year were compared to those obtained with several N fertilizer rates (0, 180, 240, and 300 kg N ha−1). Previous PS applications resulted in N fertilizer replacement values that ranged from 226 to 306 kg N ha−1. The N budget in the fifth year indicated that there had been additional uncontrolled mineral N inputs in the PS treatments in comparison to mineral N treatments. These inputs were presumed to be associated with the residual effect of PS treatments applied during the previous 4 yr. In Mediterranean environments cumulative mineralization of repeated PS applications should be considered when making fertilizer recommendations. Nitrate leaching did not differ between the treatment with the lowest PS rate (30 Mg ha−1) and the fertilization rate of 300 kg N ha−1, while higher PS rates increased nitrate leaching. Pig slurry rates above 30 to 40 Mg ha−1yr−1are not environmentally sustainable in Mediterranean agricultural systems.
Yield Response to Different Planting Geometries in Maize–Soybean Relay Strip Intercropping Systems
Authors: Yang Feng , Wang Xiaochun , Liao Dunping , Lu Fengzhi , Gao Rencai , Liu Weiguo , Yong Taiwen , Wu Xiaoling , Du Junbo , Liu Jiang , Yang Wenyu
Published: December 2014

Planting geometries directly affect crop yields in intercropping systems. Two different field experiments were conducted in 2012–2013 to analyze how different planting geometries in maize (Zea mays L.) and soybean [Glycine max (L.) Merr.] relay strip intercropping systems at 2:2 maize‐to‐soybean affect yields. Maize plants were planted in narrow‐row planting patterns, whereas soybean was planted in wide rows. The effects of bandwidth, row spacing, plant spacing, and the distance between maize and soybean rows on crop yields were studied. Total intercrop yields were higher than those of sole crop maize and soybean, and the land equivalent ratios of the intercropping systems were above 1.3. The yield of the intercropped maize increased with bandwidth reduction at the same plant density, and similar results were found with increased maize narrow‐row spacing at the same bandwidth. Plant spacing had a dominant function when the bandwidth of the intercropped soybean was >200 cm. By contrast, the distance between maize and soybean rows had a dominant function when bandwidth was <200 cm. The optimum bandwidth and maize narrow‐row spacing in maize–soybean relay intercropping systems were 200 and 40 cm, respectively. These results suggest that the appropriate reduction in the spacing of the narrow maize rows and increase in the distance between maize and soybean rows could be used to achieve high yields in maize–soybean intercropping.
Biomass Yield Enhancement Required for a Replacement Switchgrass Variety
Authors: Haankuku Choolwe , Epplin Francis M.
Published: December 2014

For perennial grasses such as switchgrass (Panicum virgatum L.) used to produce biomass for biorefineries, the replacement of an existing stand with a new variety may require the loss of a year of production. If the opportunity cost of production is considered, a new cultivar (challenger) expected to result in only a modest yield increase relative to the existing variety (defender) may fail to achieve the clearly superior criterion required by variety release committees. The objective of the study is to determine the minimum expected yield increase in a new switchgrass variety that is required to economically justify the replacement of the defender. An economic model based on capital budgeting analysis is developed. Sensitivity of the expected yield increment was examined with respect to the discount rate, biomass price, field costs, and planning horizon. Results were obtained for estimated defender yields of 16.25 and 24.0 Mg ha−1. The required yield increment is inversely related to the length (years) of the planning horizon and to the price of the biomass and is positively related to costs and the discount rate. For the base parameter levels, (a defender yield of 16.25 Mg ha−1, biomass price of US$53 Mg−1, discount rate of 5%, and planning horizon of 20 yr), a 15% yield increase of 2.4 Mg ha−1 would be required to justify replacement. Economic assessments are important to both producers and breeders when quantifying yield targets for enhanced cultivars.
Canadian Retirement Incomes: How Much Do Financial Market Returns Matter?
Authors: MacDonald Bonnie-Jeanne , Osberg Lars
Published: December 2014

How much might poor financial market returns affect the financial well-being of Canadian seniors? We compare three scenarios: if Canadian financial markets (a) never experienced the financial crisis of 2008 (i.e., continued on their pre-2008 path); (b) experienced the crisis and return to historical trends; or (c) enter a new low normal of depressed stock market returns and continued low interest rates. Using a population microsimulation model, we model the first order impacts—that is, before behavioural responses such as delayed retirement or increased savings—on the retirement income flows of Baby Boom retirees. While annual income from private savings of the median Canadian baby-boom senior drops by over half in the event of continuing low financial market returns, median financial welfare drops by only just over a fifth. Rising social transfers and stable income sources (such as Canada/Quebec Pension Plan and implicit income from home ownership) partially shield Canadian seniors from financial market risk. Canadian research has long recognized that the Canadian social pension system protects poorer Canadian seniors from destitution. Our results indicate that it also helps shield the Canadian elderly population as a whole from financial market risk.
Platonic Myth and Urban Space: City-Form as an Allegory
Authors: Akkerman Abraham
Published: December 2014

Shaping civilization across the ages, the myth of the Ideal City has reverberated through Western city-form from Plato to this day. While the intrinsic structure of Plato’s Ideal City was mirrored in the perceived constitution of the human soul, the physical design of the Ideal City, as outlined in Plato’s legend of Atlantis, corresponds to his vision of the universe at the very end of the Republic. The Platonic attempt to emulate universal perfection in the Ideal City has been manifest throughout the history of the city. It grew hand in hand with a companion allegory – that of the Grand Designer. Whereas the inherently masculine paradigms of the Ideal City and the Grand Designer have shaped Western city-form across historic times since antiquity, the feminine myth of the Garden has been all but excluded from a design expression in the city.
Frye and Hegel
Authors: Denham Robert D.
Published: December 2014

This article traces the influence of Hegel upon Frye’s thought, beginning with the extraordinary paper he wrote on romanticism as a twenty-year-old undergraduate and continuing through his two books on the Bible, The Great Code and Words with Power and his posthumously published The Double Vision. It seeks to demonstrate what Frye means by saying, “If Hegel had written his Phenomenology in mythos-language instead of in logos-language a lot of my work would be done for me.” Particular attention is paid to the ways the Hegelian notion of Aufhebung plays out in Frye’s dialectic, which characteristically works to resolve the opposition between two categories. The article also considers the importance of the ladder metaphor in both Hegel and Frye.
A Literary-Biographical Approach to the Study of Conspiracy Theory: The Development of the “Grand Design” in the Works of Douglas Reed
Authors: Lafferty David
Published: December 2014

This case study, a literary-biographical analysis of the early nonfiction works of conspiracy theorist Douglas Reed (1895–1976), is intended as a contribution to both conspiracy theory studies and the study of nonfiction narrative. My argument is that Reed’s oeuvre, understood diachronically and as an ultimately teleological whole, provides privileged insight into how conspiracy narratives are created, what happens when they come into conflict, and how new and larger conspiracy narratives are synthesized. Further, Reed’s work demonstrates that if there is a “standard” anti-Semitic conspiracy narrative, its manifestations are not homogenous and are at times subject to radical modification, with such modifications occurring during a conspiracy theorist’s processes of investigation and reinvestigation, as initially held theories connect and conflict with the deeper structures of the standard anti-Semitic conspiracy narrative and create unique synthetic variations.
Refugee Hotels: The Discourse of Hospitality and the Rise of Immigration Detention in Canada
Authors: Dawson Carrie
Published: December 2014

While serving as Minister of Citizenship and Immigration Canada between 2008 and 2013, Jason Kenney likened the detention facilities used to house an increasing number of asylum seekers and non-status migrants to hotels. And yet, when addressing the responsibilities of citizenship, he repeatedly argued that “Canada is not a hotel.” However contradictory, Kenney’s references to hotels and, implicitly, to the comforts and privileges they represent, draw on the idea of Canadian hospitality: the suggestion is that we detain asylum seekers in hotels or hotel-like conditions because we are an hospitable people but that our reputation for hospitality leaves us vulnerable to migrants who construe themselves as hotel guests with privileges rather than citizens with responsibilities. Paying particular attention to recent legislative reforms that will almost certainly result in the incarceration of more asylum seekers, this article asks how Canadian hospitality is defined and practiced today. More generally, it uses discourse analysis to explore the tension between the Canadian ideal of hospitality and the realities of an expanding immigration detention system.
“History, a Theatre of Illusions”: Texts and Contexts of Eco’s The Book of Legendary Lands
Authors:   REVIEW ESSAY, Capozzi Rocco
Published: December 2014

Umberto Eco is at his best when he teaches, entertains, and shows off his interdisciplinary and encyclopedic knowledge. It is all part of his art of docere et delectare. His novels and his essays are all about knowing more about our history, our society, our culture, and our world, including those of imaginary lands. The numerous colorful illustrations that accompany The Book of Legendary Lands make this recent publication the fourth encyclopedic illustrated text – after The History of Beauty, The History of Ugliness, and The Vertigo of Lists – and another testimonial of Eco’s love for interdisciplinary research. Eco has also had a long history of loving to examine fakes and forgeries – a familiar topic recurring often in both his scientific and creative writings. It is his love for analyzing “The Force of Falsity” in our history (the false not necessarily in the form of lies but also in the form of error) that has motivated Eco to publish his research on how curiosity, imagination, errors, and serendipity are at the foundation of many of the discoveries throughout the centuries. Imaginary and fake maps, monsters, islands, civilizations, documents, languages, secrets, and perfect worlds all come under scrutiny as Eco with his familiar wit and irony narrates and documents the history of legendary lands from Plato to our times.