bluuebunny/crossref_metadata_2025 huggingface dataset:
BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences
Authors: Bao Ergude , Jiang Tao , Girke Thomas
Published: March 2013

Motivation:  De novo transcriptome assemblies of RNA-Seq data are important for genomics applications of unsequenced organisms. Owing to the complexity and often incomplete representation of transcripts in sequencing libraries, the assembly of high-quality transcriptomes can be challenging. However, with the rapidly growing number of sequenced genomes, it is now feasible to improve RNA-Seq assemblies by guiding them with genomic sequences.

Results: This study introduces BRANCH, an algorithm designed for improving de novo transcriptome assemblies by using genomic information that can be partial or complete genome sequences from the same or a related organism. Its input includes assembled RNA reads (transfrags), genomic sequences (e.g. contigs) and the RNA reads themselves. It uses a customized version of BLAT to align the transfrags and RNA reads to the genomic sequences. After identifying exons from the alignments, it defines a directed acyclic graph and maps the transfrags to paths on the graph. It then joins and extends the transfrags by applying an algorithm that solves a combinatorial optimization problem, called the Minimum weight Minimum Path Cover with given Paths. In performance tests on real data from Caenorhabditis elegans and Saccharomyces cerevisiae, assisted by genomic contigs from the same species, BRANCH improved the sensitivity and precision of transfrags generated by Velvet/Oases or Trinity by 5.1–56.7% and 0.3–10.5%, respectively. These improvements added 3.8–74.1% complete transcripts and 8.3–3.8% proteins to the initial assembly. Similar improvements were achieved when guiding the BRANCH processing of a transcriptome assembly from a more complex organism (mouse) with genomic sequences from a related species (rat).

Availability: The BRANCH software can be downloaded for free from this site: http://manuals.bioinformatics.ucr.edu/home/branch.

Contact:  thomas.girke@ucr.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Detecting biomarkers in habitable-zone earths transiting white dwarfs
Authors: Loeb Abraham , Maoz Dan
Published: March 2013

The characterization of the atmospheres of habitable-zone Earth-mass exoplanets that transit across main-sequence stars, let alone the detection of biomarkers in their atmospheres, will be challenging even with future facilities. It has been noted that white dwarfs (WDs) have long-lived habitable zones and that a large fraction of WDs may host planets. We point out that during a transit of an Earth-mass planet across a WD, the planet's atmospheric transmission spectrum obtains a much higher contrast over the stellar background compared to a main-sequence host, because of the small surface area of the WD. The most prominent bio-marker in the present-day terrestrial atmosphere, molecular oxygen, is readily detectable in a WD transit via its A-band absorption at ∼ 0.76 μm. A potentially life-sustaining Earth-like planet transiting a WD can be found by assembling a suitable sample of ∼500 WDs and then surveying them for transits using small telescopes. If and when a transiting case is found, the O2 absorption in the planetary atmospheric transmission spectrum would be detectable with the James Webb Space Telescope (JWST) in about 5 h of total exposure time, integrated over 160 two-minute transits. Characterization of the planet atmosphere using other tracers such as water vapour and CO2 will be considerably easier. We demonstrate this future discovery space by simulating a possible transmission spectrum that would be detectable with JWST.
Detection of Candida species resistant to azoles in the microbiota of rheas (Rhea americana): possible implications for human and animal health
Authors: Brilhante Raimunda Sâmia Nogueira , de Alencar Lucas Pereira , Cordeiro Rossana de Aguiar , Castelo-Branco Débora de Souza Collares Maia , Teixeira Carlos Eduardo Cordeiro , Macedo Ramila de Brito , Lima Daniel Teixeira , Paiva Manoel de Araújo Neto , Monteiro André Jalles , Alves Nilza Dutra , Franco de Oliveira Moacir , Sidrim José Júlio Costa , Rocha Marcos Fábio Gadelha , Bandeira Tereza de Jesus Pinheiro Gomes , Rodrigues Terezinha de Jesus Santos
Published: March 2013

There is growing interest in breeding rheas (Rhea americana) in Brazil. However, there are no data on the yeast microbiota of the gastrointestinal tract of this avian species, and the phenotypic characteristics of these yeasts are not known. Therefore, the aim of this work was to isolateCandidaspecies from the digestive tract of rheas and to evaluate thein vitroantifungal susceptibility and secretion of phospholipases of the recovered isolates. For this purpose, 58 rheas from breeding operations in the cities of Fortaleza and Mossoró, north-eastern Brazil, were used. Samples were gathered from the oropharynx and cloaca of the animals using sterile swabs. Stool samples were collected from their pens by scraping with a scalpel blade. For the primary isolation, the material was seeded onto 2 % Sabouraud dextrose agar supplemented with chloramphenicol (0.5 g l−1). The isolates were identified based on morphological and biochemical features. After identification, all the strains were submitted to antifungal susceptibility testing for amphotericin B, itraconazole and fluconazole. The phospholipase activity of theCandidaspecies isolates was also tested by culturing on egg yolk agar.Candidaspecies were isolated from at least one anatomical site in 36/58 birds (14/17 juveniles and 22/41 adults) and in 6/10 faecal samples. Mostly, only a single species was isolated from each collection site (36/56 positive sites), with up to three species being observed only in four cases (4/56). A total of 77 isolates were obtained, belonging to the speciesCandida parapsilosis sensu lato(19),Candida albicans(18),Candida tropicalis(13),Candida guilliermondii(12),Candida krusei(10) andCandida famata(5).C. albicanswas more prevalent in the oropharynx of the juvenile rheas when compared with adult ones (P<0.001). All tested isolates were susceptible to amphotericin B, but 16 isolates were simultaneously resistant to the two azole derivatives (11/18C. albicans, 1/10C. krusei, 2/19C. parapsilosis sensu latoand 2/13C. tropicalis).C. albicanspresented a particularly high resistance rate to fluconazole (15/18) and itraconazole (13/18). Finally, 23/77 strains secreted phospholipases. In summary, healthy rheas carry potentially pathogenicCandidaspecies in their gastrointestinal tract, including azole-resistant strains that secrete phospholipases, and are prone to disseminating them in the environment. Thus, breeding and handling these animals may have some implications for human and animal health.
Specialized Roles of the Conserved Subunit OST3/6 of the Oligosaccharyltransferase Complex in Innate Immunity and Tolerance to Abiotic Stresses
Authors: Farid Akhlaq , Malinovsky Frederikke Gro , Veit Christiane , Schoberer Jennifer , Zipfel Cyril , Strasser Richard
Published: March 2013

Asparagine-linked glycosylation of proteins is an essential cotranslational and posttranslational protein modification in plants. The central step in this process is the transfer of a preassembled oligosaccharide to nascent proteins in the endoplasmic reticulum by the oligosaccharyltransferase (OST) complex. Despite the importance of the catalyzed reaction, the composition and the function of individual OST subunits are still ill defined in plants. Here, we report the function of the highly conserved OST subunit OST3/6. We have identified a mutant in the OST3/6 gene that causes overall underglycosylation of proteins and affects the biogenesis of the receptor kinase EF-TU RECEPTOR involved in innate immunity and the endo-β-1,4-glucanase KORRIGAN1 required for cellulose biosynthesis. Notably, the ost3/6 mutation does not affect mutant variants of the receptor kinase BRASSINOSTEROID-INSENSITIVE1. OST3/6 deficiency results in activation of the unfolded protein response and causes hypersensitivity to salt/osmotic stress and to the glycosylation inhibitor tunicamycin. Consistent with its role in protein glycosylation, OST3/6 resides in the endoplasmic reticulum and interacts with other subunits of the OST complex. Together, our findings reveal the importance of Arabidopsis (Arabidopsis thaliana) OST3/6 for the efficient glycosylation of specific glycoproteins involved in different physiological processes and shed light on the composition and function of the plant OST complex.
Imaging interfacial micro- and nano-bubbles by scanning transmission soft X-ray microscopy
Authors: Zhang Lijuan , Zhao Binyu , Xue Lian , Guo Zhi , Dong Yaming , Fang Haiping , Tai Renzhong , Hu Jun
Published: March 2013

Synchrotron-based scanning transmission soft X-ray microscopy (STXM) with nanometer resolution was used to investigate the existence and behavior of interfacial gas nanobubbles confined between two silicon nitride windows. The observed nanobubbles of SF6and Ne with diameters smaller than 2.5 µm were quite stable. However, larger bubbles became unstable and grew during the soft X-ray imaging, indicating that stable nanobubbles may have a length scale, which is consistent with a previous report using atomic force microscopy [Zhanget al.(2010),Soft Matter,6, 4515–4519]. Here, it is shown that STXM is a promising technique for studying the aggregation of gases near the solid/water interfaces at the nanometer scale.
Enhanced protection against pulmonary mycobacterial challenge by chitosan‐formulated polyepitope gene vaccine is associated with increased pulmonary secretory IgA and gamma‐interferon+ T cell responses
Authors: Ai Wenqing , Yue Yan , Xiong Sidong , Xu Wei
Published: March 2013

Induction of local (pulmonary) immunity plays a critical role in preventing dissemination of Mycobacterium tuberculosis (M. tb) during the early infection stage. To induce specific mucosal immunity, chitosan, a natural cationic polysaccharide, was employed as a mucosal gene carrier and complexed with pHSP65pep, our previously constructed multi‐epitope gene vaccine, which induces splenic gamma‐interferon (IFN‐γ)+ T helper cell 1 responses. The resultant chitosan–pHSP65pep was administered intranasally to BALB/c mice with four doses of 50 μg DNA followed by mycobacterial challenge 4 weeks after the final immunization. It was found that the chitosan formulation significantly induced production of secretory immunoglobulin A (P < 0.05) as determined by measuring its concentrations in lung lavage fluid and enhanced pulmonary CD4+ and CD8+IFN‐γ+ T cell responses (P < 0.001) compared with naked gene vaccine. Improved protection against Mycobacterium bovis bacillus Calmette–Guérin (BCG) challenge was consistently achieved by the chitosan–DNA formulation both as the vaccine alone or in a BCG prime‐vaccine boost immunization scenario. Our study shows that mucosal delivery of gene vaccine in a chitosan formulation remarkably enhances specific SIgA concentrations and mucosal IFN‐γ+ T cell response, which correlated positively with immunological protection.
Bioactive alkaloids in vertically transmitted fungal endophytes
Authors: Panaccione Daniel G. , Beaulieu Wesley T. , Cook Daniel
Published: March 2013

Plants form mutualistic symbioses with a variety of microorganisms including endophytic fungi that live inside the plant and cause no overt symptoms of infection. Some endophytic fungi form defensive mutualisms based on the production of bioactive metabolites that protect the plant from herbivores in exchange for a protected niche and nutrition from the host plant. Key elements of these symbioses are vertical transmission of the fungus through seed of the host plant, a narrow host range, and production of bioactive metabolites by the fungus.

Grasses frequently form symbioses with endophytic fungi belonging to the familyClavicipitaceae. These symbioses have been studied extensively because of their significant impacts on insect and mammalian herbivores. Many of the impacts are likely due to the production of four classes of bioactive alkaloids – ergot alkaloids, lolines, indole‐diterpenes and peramine – that are distributed in different combinations among endophyte taxa.

Several legumes, including locoweeds, are associated with a toxic syndrome called locoism as a result of their accumulation of swainsonine. Species in two genera were recently found to contain previously undescribed endophytic fungi (Undifilumspp., familyPleosporaceae) that are the source of that toxin. The fungi are strictly vertically transmitted and have narrow host ranges.

Some plant species in the morning glory family (Convolvulaceae) also form symbioses with endophytic fungi of theClavicipitaceae that produce ergot alkaloids and, perhaps in at least one case, lolines. Other species in this plant family form symbioses with undescribed fungi that produce swainsonine. The swainsonine‐producing endophytes associated with theConvolvulaceae are distinct from theUndifilumspp. associated with locoweeds and theClavicipitaceous fungi associated with Convolvulaceae.

In the establishment of vertically transmitted symbioses, fungi must have entered the symbiosis with traits that were immediately useful to the plant. Bioactive metabolites are likely candidates for such pre‐adapted traits which were likely useful to the free‐living fungi as well. With future research, vertically transmitted fungi from diverse clades with narrow host ranges and that produce bioactive compounds are likely to be found as important mutualists in additional plants.
Downstairs drivers ‐ root herbivores shape communities of above‐ground herbivores and natural enemies via changes in plant nutrients
Authors: Johnson Scott N. , Mitchell Carolyn , McNicol James W. , Thompson Jacqueline , Karley Alison J.
Published: March 2013

Terrestrial food webs are woven from complex interactions, often underpinned by plant‐mediated interactions between herbivores and higher trophic groups. Below‐ and above‐ground herbivores can influence one another via induced changes to a shared host plant, potentially shaping the wider community. However, empirical evidence linking laboratory observations to natural field populations has so far been elusive.

This study investigated how root‐feeding weevils (Otiorhynchus sulcatus) influence different feeding guilds of herbivore (phloem‐feeding aphids,Cryptomyzus galeopsidis, and leaf‐chewing sawflies,Nematus olfaciens) in both controlled and field conditions.

We hypothesized that root herbivore‐induced changes in plant nutrients (C, N, P and amino acids) and defensive compounds (phenolics) would underpin the interactions between root and foliar herbivores, and ultimately populations of natural enemies of the foliar herbivores in the field.

Weevils increased field populations of aphids by ca. 700%, which was followed by an increase in the abundance of aphid natural enemies. Weevils increased the proportion of foliar essential amino acids, and this change was positively correlated with aphid abundance, which increased by 90% on plants with weevils in controlled experiments.

In contrast, sawfly populations were 77% smaller during mid‐June and adult emergence delayed by >14 days on plants with weevils. In controlled experiments, weevils impaired sawfly growth by 18%, which correlated with 35% reductions in leaf phosphorus caused by root herbivory, a previously unreported mechanism for above‐ground–below‐ground herbivore interactions.

This represents a clear demonstration of root herbivores affecting foliar herbivore community composition and natural enemy abundance in the field via two distinct plant‐mediated nutritional mechanisms. Aphid populations, in particular, were initially driven by bottom‐up effects (i.e. plant‐mediated effects of root herbivory), but consequent increases in natural enemies triggered top‐down regulation.
Remifentanil target‐controlled infusion during second stage labour in high‐risk parturients: a case series
Authors: SCHWARZ G. L. , VOLMANEN P. , ALBRECHTSEN S. , BJOERNESTAD E.
Published: March 2013

Background

Providing adequate analgesia and appropriate sedation to high‐risk parturients during late second stage labour without compromising foetal safety remains a major challenge, especially in situations when neuraxial block is not applicable. Remifentanil emerged as an option for labour analgesia during the last decade but may be suitable for the facilitation of complicated vaginal deliveries as well.

Methods

A retrospective chart review of nine labouring women with significant medical and/or obstetrical risk factors was conducted. According to the assessment of an experienced obstetrician, vaginal delivery could only be achieved with profound analgesia, and neuraxial block was not possible because of contraindications, technical failure, or shortage of time. Mode of delivery, need for neonatal resuscitation, maternal and neonatal vital parameters, drug consumption, and personnel resource expenses were recorded.

Results

Remifentanil target‐controlled infusion (TCI) facilitated vaginal delivery in eight out of nine women. No serious adverse events were observed, but three newborns needed initial respiratory support for a few minutes. The total cost of remifentanil TCI administration to facilitate vaginal delivery compared with the estimated additional cost of an emergency caesarean section was negligible.

Conclusion

This case series suggests that remifentanil TCI may be used to facilitate vaginal delivery in high‐risk parturients when other forms of analgesia are limited. However, the small number of patients studied does not allow generalisation of the results; neither can safety concerns be dispelled yet.
DNA damage in normally and prematurely aged mice
Authors: Maslov Alexander Y. , Ganapathi Shireen , Westerhof Maaike , Quispe‐Tintaya Wilber , White Ryan R. , Van Houten Bennett , Reiling Erwin , Dollé Martijn E. T. , van Steeg Harry , Hasty Paul , Hoeijmakers Jan H. J. , Vijg Jan
Published: March 2013

Steady‐state levels of spontaneous DNA damage, the by‐product of normal metabolism and environmental exposure, are controlled by DNA repair pathways. Incomplete repair or an age‐related increase in damage production and/or decline in repair could lead to an accumulation of DNA damage, increasing mutation rate, affecting transcription, and/or activating programmed cell death or senescence. These consequences of DNA damage metabolism are highly conserved, and the accumulation of lesions in the DNA of the genome could therefore provide a universal cause of aging. An important corollary of this hypothesis is that defects in DNA repair cause both premature aging and accelerated DNA damage accumulation. While the former has been well‐documented, the reliable quantification of the various lesions thought to accumulate in DNA during aging has been a challenge. Here, we quantified inhibition of long‐distance PCR as a measure of DNA damage in liver and brain of both normal and prematurely aging, DNA repair defective mice. The results indicate a marginal, but statistically significant, increase in spontaneous DNA damage with age in normal mouse liver but not in brain. Increased levels of DNA damage were not observed in the DNA repair defective mice. We also show that oxidative lesions do not increase with age. These results indicate that neither normal nor premature aging is accompanied by a dramatic increase in DNA damage. This suggests that factors other than DNA damage per se, for example, cellular responses to DNA damage, are responsible for the aging phenotype in mice.
A Joint Regression Analysis for Genetic Association Studies with Outcome Stratified Samples
Authors: Wu Colin O. , Zheng Gang , Kwak Minjung
Published: March 2013

Genetic association studies in practice often involve multiple traits resulting from a common disease mechanism, and samples for such studies are often stratified based on some trait outcomes. In such situations, statistical methods using only one of these traits may be inadequate and lead to under‐powered tests for detecting genetic associations. We propose in this article an estimation and testing procedure for evaluating the shared‐association of a genetic marker on the joint distribution of multiple traits of a common disease. Specifically, we assume that the disease mechanism involves both quantitative and qualitative traits, and our samples could be stratified based on the qualitative trait. Through a joint likelihood function, we derive a class of estimators and test statistics for evaluating the shared genetic association on both the quantitative and qualitative traits. Our simulation study shows that the joint likelihood test procedure is potentially more powerful than association tests based on separate traits. Application of our proposed procedure is demonstrated through the rheumatoid arthritis data provided by the Genetic Analysis Workshop 16 (GAW16).
Revisiting the Fantasy–Reality Distinction: Children as Naïve Skeptics
Authors: Woolley Jacqueline D. , E. Ghossainy Maliki
Published: March 2013

Far from being the uncritical believers young children have been portrayed as, children often exhibit skepticism toward the reality status of novel entities and events. This article reviews research on children's reality status judgments, testimony use, understanding of possibility, and religious cognition. When viewed from this new perspective it becomes apparent that when assessing reality status, children are as likely to doubt as they are to believe. It is suggested that immature metacognitive abilities are at the root of children's skepticism, specifically that an insufficient ability to evaluate the scope and relevance of one's knowledge leads to an overreliance on it in evaluating reality status. With development comes increasing ability to utilize a wider range of sources to inform reality status judgments.
The effect of chronic twice daily exenatide treatment on β‐cell function in new onset type 2 diabetes
Authors: Gastaldelli Amalia , Brodows Robert G. , D'Alessio David
Published: March 2013

Objective

To determine the effect of chronic daily exenatide treatment on β‐cell function in type 2 diabetes (T2DM).

Background

Glucagon‐like peptide receptor agonists, such as exenatide, are commonly used to treat patients with T2DM. Drugs in this class are insulinotropic but lower blood glucose by multiple mechanisms such that effects on β‐cell function can be difficult to discern by conventional measures.

Design

Seventy‐nine subjects with previously untreated T2DM were studied before and after 24 weeks of treatment with one of the two doses of exenatide, 5‐ or 10‐μg twice daily, or placebo. All subjects had oral glucose tolerance tests (OGTT) before and after randomization with measurement of plasma glucose, insulin and C‐peptide concentrations. Insulin secretion rates (ISR), peripheral insulin sensitivity (OGIS) and hepatic insulin resistance index (Hep‐IR) were calculated.

Results

During the trial, all three groups lost similar, small but significant, amounts of weight. Compared to placebo, 24 weeks of daily high‐ or low‐dose exenatide treatment reduced HbA1c and improved fasting and postprandial hyperglycaemia. Exenatide was associated with improved OGIS and Hep‐IR independent of changes in weight. Plasma insulin levels and ISR during the OGTT did not differ before or after treatment with exenatide or placebo. However, when considered as a function of plasma glucose and insulin sensitivity, both doses of exenatide improved ISR proportionately to the improvement in plasma glucose. The higher dose of exenatide was associated with a significant improvement in β‐cell sensitivity to glucose.

Conclusions

These findings demonstrate that in persons with early T2DM, chronic treatment with exenatide enhanced ISR and increased β‐cell sensitivity to glucose. These improvements in β‐cell function were not clearly reflected in plasma insulin and C‐peptide levels, but became apparent when glycemia and insulin sensitivity were accounted for.
Beckwith–Wiedemann and Silver–Russell syndromes: opposite developmental imbalances in imprinted regulators of placental function and embryonic growth
Authors: Jacob KJ , Robinson WP , Lefebvre L
Published: March 2013

Beckwith–Wiedemann syndrome (BWS) and Silver–Russell syndrome (SRS) are two congenital disorders with opposite outcomes on fetal growth, overgrowth and growth restriction, respectively. Although both disorders are heterogeneous, most cases of BWS and SRS are associated with opposite epigenetic or genetic abnormalities on 11p15.5 leading to opposite imbalances in the expression levels of imprinted genes. In this article, we review evidence implicating these genes in the developmental regulation of embryonic growth and placental function in mouse models. The emerging picture suggests that both SRS and BWS can be caused by the simultaneous and opposite deregulation of two groups of imprinted genes on 11p15.5. A detailed description of the phenotypic abnormalities associated with each syndrome must take into consideration the developmental functions of each gene involved.
Active Tactile Sensibility of Single‐Tooth Implants versus Natural Dentition: A Split‐Mouth Double‐Blind Randomized Clinical Trial
Authors: Kazemi Mahmoud , Geramipanah Farideh , Negahdari Ramin , Rakhshan Vahid
Published: March 2013

Background

Unlike passive sensitivity of implants/teeth that is assessed more, only three controversial studies have compared active tactile sensibility (ATS) of implants and teeth.

Purpose

We aimed to explore the difference between the ATS of teeth and single‐tooth implants.

Methods

The ATS of single‐tooth implants and contralateral teeth was measured in 25 patients after they bit on gold and placebo foils 0‐ to 70‐μm thick, each for five times, in a random order blinded to patients and assessor, carried out at two sessions. Based on the experimental range of 0 μm (mock trials) to 70 μm, the sigmoid shape of psychometric curve was estimated to locate the 50% values as the ATS thresholds for each tooth or implant. ATS Data were analyzed using paired and unpaired t‐tests and multiple linear regression (α = 0.05, β ≤ 0.1). Also, equivalence testing approach was used to assess semi‐objectively the clinical significance.

Results

Average ATS values for teeth and implants were 21.4 ± 6.55 μm and 30.0 ± 7.55 μm, respectively (p = .0001 [paired t‐test]). None of the geometric characteristics of implants nor duration of implant in function were correlated with the ATS (p > .4 [regression]). Age was positively associated with the ATS of both implants and teeth (p ≤ .019 [regression]). Tooth ATS (but not implant ATS) was significantly higher in males compared with females (p = .050 [unpaired t‐test]), which contributed to a generalizable tooth‐implant difference higher than 8‐μm clinical equivalence margin in females. The ATS was not significantly different between arches or between anterior/posterior regions (p > .6).

Conclusion

There was a slight but statistically significant difference between implant and tooth tactile sensitivities.
Constructing a New Theory From Old Ideas and New Evidence
Authors: Rhodes Marjorie , Wellman Henry
Published: March 2013

A central tenet of constructivist models of conceptual development is that children's initial conceptual level constrains how they make sense of new evidence and thus whether exposure to evidence will prompt conceptual change. Yet little experimental evidence directly examines this claim for the case of sustained, fundamental conceptual achievements. The present study combined scaling and experimental microgenetic methods to examine the processes underlying conceptual change in the context of an important conceptual achievement of early childhood—the development of a representational theory of mind. Results from 47 children (M age = 3.7 years) indicate that only children who were conceptually close to understanding false belief at the beginning of the study, and who were experimentally exposed to evidence of people acting on false beliefs, reliably developed representational theories of minds. Combined scaling and microgenetic data revealed how prior conceptual level interacts with experience, thereby providing critical experimental evidence for how conceptual change results from the interplay between conceptions and evidence.
A Paradox for Conservation: Electricity Pylons May Benefit Avian Diversity in Intensive Farmland
Authors: Tryjanowski Piotr , Sparks Tim H. , Jerzak Leszek , Rosin Zuzanna M. , Skórka Piotr
Published: March 2013

Over the past century, electricity power lines have been a conspicuous part of the European landscape. These structures are generally known to cause fatalities to birds. However, some bird species use electricity poles as nesting structures, song posts, or for perching. Other, but not‐acknowledged, benefits probably include the marginal habitats around the base of pylons. We tested differences in breeding bird communities under pylons, under electricity high‐voltage power lines, and in adjacent open fields. Birds were counted twice during the 2011 breeding season in a total of 91 study plots located in the intensive farmland of western Poland. Both species number and bird abundance were significantly higher under pylons and under power lines at control points than in open fields, especially where there were shrubs under the pylons. Pylons and power lines locally may play a positive role for the avian community in intensive farmland, especially if vegetation succession under pylons is allowed to develop to the shrub stage.
Understanding the Determinants of Volunteer Retention Through Capture‐Recapture Analysis: Answering Social Science Questions Using a Wildlife Ecology Toolkit
Authors: Beirne Christopher , Lambin Xavier
Published: March 2013

Scientists and conservationists increasingly rely on contributions by volunteers recruited from the wider public to work over large and ecologically meaningful spatial scales. Optimizing working in partnership with unpaid, volunteer citizen scientists and conservationists requires an understanding of the determinants of volunteer retention rates and how they are affected by management practices. To this effect, we present the novel use of the mark‐recapture framework widely used in wildlife demography in order to quantify volunteer retention probabilities. We illustrate the versatility and power of the approach using a project that removed invasive American mink from 10,000 km2 in Scotland in partnership with volunteer citizen conservationists recruited from local communities. Wide scale adoption of the mark‐recapture framework to analyze volunteer management will give novel insights into how volunteers interact with the conservation projects they are involved in and provide evidence for their optimal management.
Why do Boards Differ? Because Owners Do: Assessing Ownership Impact on Board Composition
Authors: Sur Sujit , Lvina Elena , Magnan Michel
Published: March 2013

Manuscript Type

Empirical

Research Question/Issue

Does the ownership structure of a firm, specifically the aggregation of the different ownership types within each firm, relate with the composition of its board?

Research Findings/Insights

Using archival data from a sample comprising 1,487 U.S. firms, we find that the composition of the individual profiles of directors on corporate boards (i.e., independent, affiliated, or insider) match a firm's aggregated ownership configuration (institutional, corporate parent, family‐entrepreneur control) even after parsing out the impact of CEO characteristics, firm size, and performance. Further analyses elaborate on the specific relationship between each director profile and ownership types present within the firm.

Theoretical/Academic Implications

This study builds upon three conceptual perspectives: agency, resource dependency, and behavioral. We argue that each type of ownership has differing imperatives and may prefer different types of directors to fulfill their governance needs. The paper illustrates that the relationship between corporate governance, specifically board composition, and ownership is a comprehensive phenomenon that is best understood through multiple theoretical lenses.

Practitioner/Policy Implications

This study shows that ownership and board composition are not substitutable governance mechanisms as commonly understood, but might be complementary mechanisms. A finding that governance mechanisms are complementary implies that regulatory or institutional pressures to modify board composition with the addition of directors with similar profiles may affect the governance in unforeseen ways.
Basaloid tumors in nevus sebaceus revisited: the follicular stem cell marker PHLDA1 (TDAG51) indicates that most are basal cell carcinomas and not trichoblastomas
Authors: Sellheyer Klaus , Cribier Bernard , Nelson Paula , Kutzner Heinz , Rütten Arno
Published: March 2013

Background

Until the 1990s, basal cell carcinoma (BCC) was viewed as the most common epithelial neoplasm developing in association with nevus sebaceus (NS). Currently, trichoblastoma is thought of as the most prevalent basaloid neoplasm in NS. The follicular stem cell marker pleckstrin homology‐like domain, family A, member 1 (PHLDA1) also known as T‐cell death‐associated gene 51 (TDAG51) labels trichoepithelioma (TE) but not BCC. Therefore, we explored its usefulness in basaloid neoplasms developing in NS.

Methods

We studied immunohistochemically PHLDA1 in 10 nodular BCCs, 11 TEs, 11 trichoblastomas and 25 NS with basaloid tumors. Additionally, we examined the expression of BCC marker BerEP4 and the distribution of Merkel cells that function as surrogate markers for benign follicular neoplasms.

Results

Nineteen of the 25 basaloid tumors in NS were PHLDA1‐negative comparable to BCC arising de novo and six tumors were PHLDA1‐positive comparable to solitary trichoblastomas and TEs. Fewer Merkel cells were seen in BCCs associated with NS when compared with trichoblastoma. BerEP4 did not discriminate between the neoplasms.

Conclusions

We raise concern that the unquestioned assessment that basaloid tumors developing in association with NS represent mostly trichoblastomas and not BCC may not be true. This influences clinical care, as it is paramount in the decision of whether to excise these lesions or not.
Regimes of Dispossession: From Steel Towns to Special Economic Zones
Authors: Levien Michael
Published: March 2013

This article compares land dispossession for industrial development under state‐developmentalism and neoliberalism in India. Drawing on interviews, ethnography and archives of industrial development agencies, it compares earlier steel towns and state‐run industrial estates with today's Special Economic Zones (SEZs) and argues that they embody different regimes of dispossession. While steel towns and industrial estates reflected a regime of land for production with pretensions of inclusive social transformation, SEZs represent a neoliberal regime of land for the market in which ‘land broker states’ have emerged to indiscriminately transfer land from peasants to capitalist firms for real estate. The present regime has been unable to achieve the ideological legitimacy of its predecessor, leading to more widespread and successful ‘land wars’. The article argues more broadly that variations in dispossession across space and time can be understood as specific constellations of state roles, economic logics tied to class interests and ideological articulations of the ‘public good’.
Indirect Dispossession: Domestic Power Imbalances and Foreign Access to Land in Mozambique
Authors: Fairbairn Madeleine
Published: March 2013

Rather than treating the global land grab as a top‐down phenomenon driven by global markets or foreign states, this article instead highlights the crucial mediating role played by the host state and domestic elites through a case study of Mozambique. I first introduce the domestic institutional framework, particularly the national Land Law and the institutions that determine the economic value of land. I then argue for an analysis of large‐scale land acquisitions that brings into focus the effects of domestic power imbalances on determining the outcomes of foreign demand for land. I examine the ways in which domestic inequality may shape foreign land acquisitions through a typology of the sources of power that give domestic elites a privileged role in relation to foreign investors. The five sources of domestic power considered are: traditional authority, bureaucratic influence, historical accumulation, locally‐based business knowledge and networks, and control over the development agenda. Finally, I conclude that the emphasis placed on the actions of the foreigner by both opponents (via framings of land acquisitions as neocolonialism or imperialism) and proponents (via solutions rooted in corporate codes of conduct) may obscure the ways in which pre‐existing domestic inequality conditions the outcomes of these deals.
Building the Politics Machine: Tools for ‘Resolving’ the Global Land Grab
Authors: Dwyer Michael B.
Published: March 2013

The recent proliferation of transnational land deals has put the long‐fraught relationship between international cooperation, national development and local dispossession back in the political spotlight. This article argues that transnational land access cannot be resolved as a political question without a better understanding of the material, legal and administrative geographies that accompany and enable it. Using evidence from Laos, the paper illustrates two tools for ‘resolving’ the global land grab geographically: first, a biographical or trajectory‐based approach that connects specific land grabs to larger development landscapes (e.g. of urban infrastructuring); and second, genealogies of property formalization that interrogate and deconstruct the legal geographies of land access, both on and off the map. The paper concludes by suggesting that these tools have purchase elsewhere as well.
Chinese Land‐Based Interventions in Senegal
Authors: Buckley Lila
Published: March 2013

As Chinese land‐based interventions multiply across the African continent, this article focuses on a single Chinese–Senegalese government‐run agriculture demonstration centre to provide insight into the daily realities of Chinese–African interactions on African land. Ethnographic methodologies are employed to examine practices and discourses on agricultural governance among Chinese and Senegalese informants. Building on theories of agriculture as performance, I show how distinct repertoires for land management are negotiated and reshaped by different subjects in a kind of improvised dance, where individuals’ improvisations lead to unanticipated project outcomes. What emerges is a picture of a Chinese agricultural management regime for African land that is simultaneously fraught with conflict, while also replete with collaboration benefiting some smallholder farmers. This actor‐oriented approach provides a critical empirical lens as well as a research framework for engaging more constructively with Chinese in large‐scale land acquisitions. I argue that ‘land grabbing’ must be seen not as a straightforward, linear process of state or corporate takeover of global land, but as a dynamic performance of negotiation among diverse state actors, corporate players and citizens — one that will reshape global development in unanticipated ways.
Road Mapping: Megaprojects and Land Grabs in the Northern Guatemalan Lowlands
Authors: Grandia Liza
Published: March 2013

From IIRSA (Integration of Regional Infrastructure in South America) to the PPP (Puebla to Panama Plan, later renamed the Mesoamerica Project), development banks are sponsoring a renewed wave of mega‐infrastructure projects across the Americas to support corporate trade and commerce. Concurrent with these are donor‐led efforts to modernize land administration systems, including a US$ 31 million World Bank loan (1998–2007) to survey and legalize settler claims in the northern Guatemalan department of Petén. Contrary to project planners’ stated goals of sustainable development, infrastructure projects have coincided with widespread land grabbing (up to 46 per cent of smallholder lands) by cattle ranchers, African palm plantations, narco traffickers, and other imbricated elites. Documenting the crossings and conjunctures of the PPP with market‐led agrarian reform, this ethnographic study suggests that the Guatemalan military may be a shadow beneficiary of new power assemblages emerging from the narco/cattle/agro‐industrial land concentration occurring in Petén.
Advantages of Real Time Three‐Dimensional Echocardiography in the Assessment of Right Ventricular Volumes and Function in Patients with Pulmonary Hypertension Compared with Conventional Two‐Dimensional Echocardiography
Authors: Di Bello Vitantonio , Conte Lorenzo , Delle Donne Maria Grazia , Giannini Cristina , Barletta Valentina , Fabiani Iacopo , Palagi Caterina , Nardi Carmela , Dini Frank Lloyd , Marconi Letizia , Paggiaro Pierluigi , Palla Antonio , Marzilli Mario
Published: March 2013

Background

In recent years, right ventricular (RV) function has acquired greater relevance as a clinical and prognostic marker in many physiopathological conditions. The study aims to point out the value of real time three‐dimensional echocardiography (RT3DE) and tissue Doppler imaging (TDI) in the evaluation of patients affected by pulmonary hypertension (PH), compared with conventional two‐dimensional (2D) echocardiography.

Methods

We enrolled 44 subjects affected by PH who underwent 2D and Doppler echocardiography, RT 3D Echocardiography and TDI evaluation of the RV, and a healthy control group. PH itself can induce severe functional and structural abnormalities of the RV, such as RV hypertrophy, RV dilation, and RV systolic and diastolic dysfunction.

Results

In this study, RV FAC, and TAPSE showed marked alterations in patients with PH compared to the control group (C): (RVFAC: [PH] 0.29 ± 0.07 vs. [C] 0.49 ± 0.05%, P < 0.0001; TAPSE: [PH] 15.3 ± 3.2 vs. [C] 21.1 ± 2.6 mm, P > 0.0001). The 3D RV end‐diastolic volume was significantly higher in PH than in C (PH) (138.7 ± 25.3 vs. [C] 82.8 ± 12.5 mL, P < 0.0001] as well as 3D RV end‐systolic volume (PH) (97.6 ± 21.5 vs. [C] 39.3 ± 9.5 mL, P < 0.0001). The 3D RV ejection fraction (EF) was significantly lower in the pulmonary hypertension group than in healthy subjects (31.8 ± 6.8 vs. [C] 52.5 ± 4.7%, P < 0.0001).

Conclusions

In patients with PH, evaluation of the RV diastolic and systolic volume and EF by RT3DE has shown a higher discriminating power in comparison, respectively, with 2DRV diastolic area and the relative fractional area changes.
Severe Obesity Impairs Systolic and Diastolic Heart Function – The Significance of Pulsed Tissue Doppler, Strain, and Strain Rate Parameters
Authors: Wierzbowska‐Drabik Karina , Chrzanowski Łukasz , Kapusta Anna , Uznańska‐Loch Barbara , Płońska Edyta , Krzemińska‐Pakuła Maria , Kurpesa Małgorzata , Rechciński Tomasz , Trzos Ewa , Kasprzak Jarosław D.
Published: March 2013

Background

We assessed the impact of morbid obesity on systolic and diastolic heart function in severely obese, but otherwise healthy subjects and age‐matched controls.

Methods

Overall, 27 obese patients: 19 female (F) and 8 male (M) mean age 37 ± 9, mean body mass index (BMI) 46 ± 6 and 27 control subjects: mean age 36 ± 10, mean BMI 23 ± 3 were examined by transthoracic echocardiography, including tissue Doppler echocardiographic (TDE) assessment and speckle tracking echocardiography to measure left ventricular longitudinal, circumferential, and radial strain (S) and strain rate (SR) during systolic and early diastolic phase.

Results

Obese patients presented with enlargement of both ventricles and the left atrium, and thicker left ventricular wall. Although left ventricular ejection fraction (EF) as well as amplitude of tricuspid annulus plane systolic excursion (TAPSE) was similar, the amplitude of mitral annulus plane systolic excursion (MAPSE) and ventricular systolic and early diastolic velocities measured by TDE were significantly lower for both ventricles in the obese group. (RV S′ 13 ± 3 cm/sec vs. 15 ± 2 cm/sec, P = 0.0057; LV S′ lat 8.5 ± 1.6 cm/sec vs. 12.1 ± 2.8, P < 0.0001, E′ lat: 12.4 ± 2.9 vs. 16.4 ± 3.5 cm/sec for left ventricular and E′ 12 ± 3 cm/sec vs. 18 ± 4 for right ventricular velocities, P < 0.0001). Among the deformation parameters, systolic and diastolic circumferential and systolic radial strain and SR were decreased in the obese subjects, whereas longitudinal strain did not differ significantly.

Conclusions

TDE parameters documented reduced systolic and diastolic function of both ventricles in obese patients. 2‐dimensional speckle tracking analysis revealed that circumferential and radial but not longitudinal strain and SR were impaired in the obese group.
B‐Type Natriuretic Peptide Predicts Left Atrial Appendage Thrombus in Patients with Nonvalvular Atrial Fibrillation
Authors: Doukky Rami , Gage Heather , Nagarajan Vijaiganesh , Demopoulos Anna , Cena Marek , Garcia‐Sayan Enrique , Karam George J. , Kazlauskaite Rasa
Published: March 2013

Purpose

To investigate whether plasma B‐type Natriuretic peptide (BNP), a surrogate of left ventricular filling pressure (LVFP), is predictive of left atrial appendage thrombus (LAAT) in patients with nonvalvular atrial fibrillation (AF) independent of known clinical risk predictors.

Methods

We conducted a retrospective cohort study of 297 consecutive subjects with AF who underwent a clinically indicated transesophageal echocardiogram (TEE) to evaluate for LAAT and spontaneous echo contrast (SEC). Among those, 136 had a clinically indicated BNP level. Using multivariate logistic regression analysis models, we determined factors independently predictive of the primary endpoint of LAAT and the secondary endpoint of either LAAT or SEC.

Results

Nineteen subjects (6.4%) had LAAT and they were found to have a higher mean CHADS2 score (2.53 vs 1.76, P = 0.01) and mean BNP level [1949 vs. 819 pg/mL, P = 0.001] than those without LAAT. None of the patients with a BNP level ≤500 pg/mL had LAAT. Multivariate logistic regression analysis demonstrated that BNP was predictive of LAAT and the composite of LAAT/SEC independent of the CHADS2 score and warfarin therapy [OR = 1.23 and 1.6 per 500 pg/mL increment in BNP, P‐values = 0.03 and 0.001; respectively]. Moreover, adding BNP to the predictive model negated the influence of the CHADS2 score.

Conclusion

These data indicate that BNP is an independent predictor of LAAT in AF and may complement the role of the CHADS2 score in predicting stroke risk.