bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subspecies delineation amid phenotypic, geographic and genetic discordance in a songbird
Authors: Walsh Jennifer , Lovette Irby J. , Winder Virginia , Elphick Chris S. , Olsen Brian J. , Shriver Gregory , Kovach Adrienne I. 
Published: January 2017

AbstractUnderstanding the processes that drive divergence within and among species is a long‐standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra‐ and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and salt marsh (Ammodramus caudacutus) sparrow complex, a group with populations that span considerable geographic distributions and a habitat gradient. We evaluated genetic structure among and within five putative subspecies of A. nelsoni and A. caudacutus using a reduced‐representation sequencing approach to generate a panel of 1929 SNPs among 69 individuals. Although we detected morphological differences among some groups, individuals sorted along a continuous phenotypic gradient. In contrast, the genetic data identified three distinct clusters corresponding to populations that inhabit coastal salt marsh, interior freshwater marsh and coastal brackish–water marsh habitats. These patterns support the current species‐level recognition but do not match the subspecies‐level taxonomy within each species—a finding which may have important conservation implications. We identified loci exhibiting patterns of elevated divergence among and within these species, indicating a role for local selective pressures in driving patterns of differentiation across the complex. We conclude that this evidence for adaptive variation among subspecies warrants the consideration of evolutionary potential and genetic novelty when identifying conservation units for this group.
Sex‐biased transcriptome divergence along a latitudinal gradient
Authors: Allen Scott L. , Bonduriansky Russell , Sgro Carla M. , Chenoweth Stephen F. 
Published: January 2017

AbstractSex‐dependent gene expression is likely an important genomic mechanism that allows sex‐specific adaptation to environmental changes. Among Drosophila species, sex‐biased genes display remarkably consistent evolutionary patterns; male‐biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex‐biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex‐specific selection and the evolution of sex‐biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male‐biased genes, there was no overrepresentation of X‐linked genes in males. By contrast, X‐linked divergence was elevated in females, especially for female‐biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro‐ and micro‐ecological spatial scales.
Trapped within the city: integrating demography, time since isolation and population‐specific traits to assess the genetic effects of urbanization
Authors: Lourenço André , Álvarez David , Wang Ian J. , Velo‐Antón Guillermo 
Published: January 2017

AbstractUrbanization is a severe form of habitat fragmentation that can cause many species to be locally extirpated and many others to become trapped and isolated within an urban matrix. The role of drift in reducing genetic diversity and increasing genetic differentiation is well recognized in urban populations. However, explicit incorporation and analysis of the demographic and temporal factors promoting drift in urban environments are poorly studied. Here, we genotyped 15 microsatellites in 320 fire salamanders from the historical city of Oviedo (Est. 8th century) to assess the effects of time since isolation, demographic history (historical effective population size; Ne) and patch size on genetic diversity, population structure and contemporary Ne. Our results indicate that urban populations of fire salamanders are highly differentiated, most likely due to the recent Ne declines, as calculated in coalescence analyses, concomitant with the urban development of Oviedo. However, urbanization only caused a small loss of genetic diversity. Regression modelling showed that patch size was positively associated with contemporary Ne, while we found only moderate support for the effects of demographic history when excluding populations with unresolved history. This highlights the interplay between different factors in determining current genetic diversity and structure. Overall, the results of our study on urban populations of fire salamanders provide some of the very first insights into the mechanisms affecting changes in genetic diversity and population differentiation via drift in urban environments, a crucial subject in a world where increasing urbanization is forecasted.
Exploring the symbiont diversity of ancient western redcedars: arbuscular mycorrhizal fungi of long‐lived hosts
Authors: Gorzelak Monika A. , Pickles Brian J. , Hart Miranda M. 
Published: January 2017

AbstractArbuscular mycorrhizal fungi (AMF) are globally distributed, monophyletic root symbionts with ancient origins. Their contribution to carbon cycling and nutrient dynamics is ecologically important, given their obligate association with over 70% of vascular plant species. Current understanding of AMF species richness and community structure is based primarily on studies of grasses, herbs and agricultural crops, typically in disturbed environments. Few studies have considered AMF interactions with long‐lived woody perennial species in undisturbed ecosystems. Here we examined AMF communities associated with roots and soils of young, mature and old western redcedar (Thuja plicata) at two sites in the old‐growth temperate rainforests of British Columbia. Due to the unique biology of AMF, community richness and structure were assessed using a conservative, clade‐based approach. We found 91 AMF OTUs across all samples, with significantly greater AMF richness in the southern site, but no differences in richness along the host chronosequence at either site. All host age classes harboured AMF communities that were overdispersed (more different to each other than expected by chance), with young tree communities most resembling old tree communities. A comparison with similar clade richness data obtained from the literature indicates that western redcedar AMF communities are as rich as those of grasses, tropical trees and palms. Our examination of undisturbed temperate old‐growth rainforests suggests that priority effects, rather than succession, are an important aspect of AMF community assembly in this ecosystem.
Understanding the formidable nail barrier: A review of the nail microstructure, composition and diseases
Authors: Baswan Sudhir , Kasting Gerald B. , Li S. Kevin , Wickett Randy , Adams Brian , Eurich Sean , Schamper Ryan 
Published: January 2017

SummaryThe topical treatment of nail fungal infections has been a focal point of nail research in the past few decades as it offers a much safer and focused alternative to conventional oral therapy. Although the current focus remains on exploring the ways of enhancing permeation through the formidable nail barrier, the understanding of the nail microstructure and composition is far from complete. This article reviews our current understanding of the nail microstructure, composition and diseases. A few of the parameters affecting the nail permeability and potential causes of the recurrence of fungal nail infection are also discussed.
A Late Bronze Age Ship from Liman Tepe with Reference to the Late Bronze Age Ships from İZMIR / Bademgediği Tepesi and Kos / Seraglio
Authors: Aykurt Ayşegül , Erkanal Hayat 
Published: January 2017

SummaryIn this article, a Mycenaean pottery sherd from Liman Tepe is discussed. The piece, which was locally produced, probably belongs to a ring‐based crater (FS 281). Comparisons with other, similar sherds suggest that warriors aboard a ship are depicted. As one of the few examples of its period decorated in this way, the sherd has been dated to the early or middle phase of LH III C, belonging to the period after the collapse of the Hittite Empire in Anatolia and the Mycenaean kingdoms in mainland Greece. The depictions on this sherd are highly significant, as they contribute to the corpus of evidence for migrations from the western to the eastern Mediterranean and the unrest which characterized the period.
Endogenous circadian rhythms in pigment composition induce changes in photochemical efficiency in plant canopies
Authors: García‐Plazaola José Ignacio , Fernández‐Marín Beatriz , Ferrio Juan Pedro , Alday Josu G. , Hoch Günter , Landais Damien , Milcu Alexandru , Tissue David T. , Voltas Jordi , Gessler Arthur , Roy Jacques , Resco de Dios Víctor 
Published: January 2017

AbstractThere is increasing evidence that the circadian clock is a significant driver of photosynthesis that becomes apparent when environmental cues are experimentally held constant. We studied whether the composition of photosynthetic pigments is under circadian regulation, and whether pigment oscillations lead to rhythmic changes in photochemical efficiency. To address these questions, we maintained canopies of bean and cotton, after an entrainment phase, under constant (light or darkness) conditions for 30–48 h. Photosynthesis and quantum yield peaked at subjective noon, and non‐photochemical quenching peaked at night. These oscillations were not associated with parallel changes in carbohydrate content or xanthophyll cycle activity. We observed robust oscillations of Chl a/b during constant light in both species, and also under constant darkness in bean, peaking when it would have been night during the entrainment (subjective nights). These oscillations could be attributed to the synthesis and/or degradation of trimeric light‐harvesting complex II (reflected by the rhythmic changes in Chl a/b), with the antenna size minimal at night and maximal around subjective noon. Considering together the oscillations of pigments and photochemistry, the observed pattern of changes is counterintuitive if we assume that the plant strategy is to avoid photodamage, but consistent with a strategy where non‐stressed plants maximize photosynthesis.
Mn accumulation in a submerged plant Egeria densa (Hydrocharitaceae) is mediated by epiphytic bacteria
Authors: Tsuji Kousuke , Asayama Takuma , Shiraki Nozomi , Inoue Shota , Okuda Erina , Hayashi Chizuru , Nishida Kazuma , Hasegawa Hiroshi , Harada Emiko 
Published: January 2017

AbstractMany aquatic plants act as biosorbents, removing and recovering metals from the environment. To assess the biosorbent activity of Egeria densa, a submerged freshwater macrophyte, plants were collected monthly from a circular drainage area in Lake Biwa basin and the Mn concentrations of the plants were analysed. Mn concentrations in these plants were generally above those of terrestrial hyperaccumulators, and were markedly higher in spring and summer than in autumn. Mn concentrations were much lower in plants incubated in hydroponic medium at various pH levels with and without Mn supplementation than in field‐collected plants. The precipitation of Mn oxides on the leaves was determined by variable pressure scanning electron microscopy‐energy dispersive X‐ray analysis and Leucoberbelin blue staining. Several strains of epiphytic bacteria were isolated from the field‐collected E. densa plants, with many of these strains, including those of the genera Acidovorax, Comamonas, Pseudomonas and Rhizobium, found to have Mn‐oxidizing activity. High Mn concentrations in E. densa were mediated by the production of biogenic Mn oxide in biofilms on leaf surfaces. These findings provide new insights into plant epidermal bacterial flora that affect metal accumulation in plants and suggest that these aquatic plants may have use in Mn phytomining.
Contact Burn with Blister Formation in Children Treated with Sennosides
Authors: Cogley Kimberly , Echevarria Andrea , Correa Catalina , De la Torre‐Mondragón Luis 
Published: January 2017

AbstractEight children treated for severe constipation with sennosides unexpectedly developed contact burns with blisters secondary to the use of these laxatives. All patients wore diapers, and the injuries occurred overnight. To avoid this side effect, we recommend that patients treated with sennosides, especially those in diapers, receive the medication at a time that allows for bowel movements to occur during the day and not overnight.
Relation between mast cells concentration and serotonin expression in chagasic megacolon development
Authors: Freitas M. A. R. , Segatto N. , Tischler N. , de Oliveira E. C. , Brehmer A. , da Silveira A. B. M. 
Published: January 2017

SummaryChagas’ disease is still reaching about 10 million people in the world. In South America, one of the most severe forms of this disease is the megacolon, characterized by severe constipation, dilated sigmoid colon and rectum and severe malnutrition. Previous data suggested that mast cells and serotonin (5‐hydroxytryptamine [5‐HT]) expression could be involved in intestinal homeostasis control, avoiding the chagasic megacolon development. The aim at this study was to characterize the presence of mast cells and expression of serotonin in chagasic patients with and without megacolon and evaluate the relation between mast cells, serotonin and megacolon development. Our results demonstrated that patients without megacolon feature a large amount of serotonin and few mast cells, while patients with megacolon feature low serotonin expression and a lot of mast cells. We believe that serotonin may be involved in the inflammatory process control, triggered by mast cells, and the presence of this substance in large quantities of the intestine could represent a mechanism of megacolon prevention.
Establishment and characterization of a coculture system of equine endometrial epithelial and stromal cells
Authors: Lapko L , Böttcher D , Theuß T , Klug J , Schoon H‐A 
Published: January 2017

ContentsTo investigate the equine endometrium as close to the in vivo situation as possible, we established a coculture system for epithelial and stromal cells (ECs/SCs). ECs and SCs were isolated from nine endometrial tissue specimens. ECs obtained as glandular formations were cultivated on one side of the semipermeable membrane of a Millicell® insert. After 2 days, SCs (2 × 104 cells/membrane) were seeded onto the other side of the same membrane. During cocultivation, the low serum containing culture medium (Theuß et al., 2010) was supplemented with different concentrations and combinations of 17β‐estradiol (2.0–3.0 pg/ml medium) and progesterone (0.5–15.0 ng/ml medium). Once the cocultures formed continuous cell layers as determined by phase‐contrast microscopy, the membranes were fixed and processed for light microscopical examination. Cytokeratin 19, steroid hormone receptors and the uterine proteins uteroglobin and calbindinD9k were detected using immunocytochemistry to determine the degree of culture purity and functional cellular differentiation. The culture purity of the EC layer averaged ≥95%. Uteroglobin and calbindinD9k were consistently expressed in ECs, while hormone receptors were predominantly absent in both cell populations. An explicit cytomorphological epithelial differentiation with formation of round‐oval to polygonal cell forms was encountered in ≤50% of all ECs and independent of supplemented steroids. Based on the findings altogether, and despite the partly absent congruence to the in situ prerequisites, we established a standardized and reproducible coculture system, which offers a basic approach for studies of physiologic and pathophysiologic issues in the mare.
Have mangrove restoration projects worked? An in‐depth study in Sri Lanka
Authors: Kodikara Kodikara Arachchilage Sunanda , Mukherjee Nibedita , Jayatissa Loku Pullukuttige , Dahdouh‐Guebas Farid , Koedam Nico 
Published: January 2017

AbstractThis study investigated the effectiveness of mangrove planting initiatives in Sri Lanka. All the lagoons and estuaries in Sri Lanka were included in the study. We documented all agencies and locations, involved in mangrove planting efforts, along with the major drivers of these planting initiatives, their extents, and the possible causes of the success or failure of planting. An adapted three‐step framework and a field survey consisting of vegetation and soil surveys and questionnaires were used to evaluate the objectives. We found that about 1,000–1,200 ha of mangroves, representing 23 project sites with 67 planting efforts, have been under restoration with the participation of several governmental and nongovernmental organizations. However, about 200–220 ha showed successful mangrove restoration. Nine out of 23 project sites (i.e. 36/67 planting efforts) showed no surviving plants. The level of survival of the restoration project sites ranged from 0 to 78% and only three sites, that is, Kalpitiya, Pambala, and Negombo, showed a level of survival higher than 50%. Survival rates were significantly correlated with post‐care. Planting mangrove seedlings at the incorrect topography often entails inappropriate soil conditions for mangroves. Survival rates showed significant correlations with a range of soil parameters except soil pH. Disturbance and stress caused by cattle trampling, browsing, algal accumulation, and insect attacks, factors that may themselves relate to choosing sites with inappropriate topography and hydrology, were common to most sites. The findings are a stark illustration of the frequent mismatch between the purported aims of restoration initiatives and the realities on the ground.
Effect of red blood cell preservation by droplet freezing with non‐permeable cryoprotective agents in blood group antigen reactivity
Authors: Chagas M. A. B. , Chaves D. G. , Haddad S. K. , Ubiali E. M. A. , Schmidt L. C. , Silva‐Malta M. C. F. 
Published: January 2017

SUMMARYBackgroundIn the last few decades, various red blood cell (RBC) freezing techniques have been developed and improved to enable the preservation of erythrocytes for future use in pre‐transfusion tests in reference immunohaematology laboratories. However, not all these techniques have been sufficiently evaluated for the preservation of blood group antigens.ObjectivesIn this study, we evaluated the antigenic pattern of RBCs preserved by droplet freezing in liquid nitrogen in a blood bank context.MethodsBlood samples were evaluated for the reactivity of blood group antigens after droplet freezing using the non‐permeable cryoprotective agent polyvinylpyrrolidone (PVP) and sucrose–dextrose (S + D) solutions.ResultsNo qualitative changes were observed in RBC reactivity after freezing and thawing for the antigens Fyb, Leb, C, E, Cw, Lua, Lub, Kpa, Kpb and Dia. However, cryopreservation using PVP resulted in a significant increase in reactivity of Fyb antigen on comparing fresh and frozen samples (P < 0·001).ConclusionThe establishment of detailed protocols for cryopreservation of RBCs, which take into account the maintenance of antigenic characteristics, is necessary to increase security in pre‐transfusion testing using frozen RBCs.
Uveal schwannoma in a brown‐eyed dog
Authors: Marlo Todd L. , Giuliano Elizabeth A. , Moore Cecil P. , Shaw Gillian C. , Teixeira Leandro B. C. 
Published: January 2017

AbstractAn eleven‐year‐old, female spayed Boxer dog was diagnosed with a uveal schwannoma (formerly known as the spindle cell tumor of the blue‐eyed dog or SCTBED) despite having a uniformly brown iris. The patient presented to emergency for ocular discomfort, and the right globe was subsequently enucleated due to glaucoma and submitted for histopathology. Upon histopathologic evaluation, a uveal schwannoma was diagnosed and confirmed with immunohistochemical staining. Complete metastatic evaluation 1 and 6 months after initial presentation did not reveal evidence of metastasis, and the dog remains systemically healthy. This case represents a unique variant of uveal schwannoma and is relevant because although the vast majority of these tumors occur in blue‐eyed dogs, clinicians should not completely rule out this tumor as a differential based on the iris color.
Variations in isotopic composition of desalinated water
Authors: Al‐Basheer Watheq , Al‐Jalal AbdulAziz , Gasmi Khaled 
Published: January 2017

AbstractVariations in isotopic ratios of water samples collected from three plants functioning on two different desalination processes were evaluated by comparing their measured δ18O, δ17O and the δ2H isotopic ratios before and after desalination using a system based on tunable off‐axis integrated‐cavity‐output diode laser spectroscopy (OA‐ICOS). The δ18O, δ17O and the δ2H isotopic ratio measurements for water samples collected before desalination are compared against their peers of desalinated water from two desalination plants on the Arabian Gulf that are operating under the Multistage Flash (MSF) process. Also, variations in the δ18O, δ17O and the δ2H isotopic ratio measurements due to desalination from a Reversal Osmosis (RO) facility in Dhahran, Saudi Arabia were also reported and compared against variations in isotopic composition of water desalinated in two MSF plants.
Embedding Every Cycle in Conditionally Faulty Folded Hypercubes
Authors: KUO CHE-NAN 
Published: January 2017

A network is said to be conditionally faulty if its every vertex is incident to at least g fault-free neighbors, where g≥1. An n-dimensional folded hypercube FQn is a well-known variation of an n-dimensional hypercube Qn, which can be constructed from Qn by adding an edge to every pair of vertices with complementary addresses. In this paper, we define that a network is said to be g-conditionally faulty if its every vertex is incident to at least g fault-free neighbors, and let FFv (respectively, FFe) denote the set of faulty vertices (respectively, faulty edges) in FQn. Then, we consider for the cycles embedding properties in FQn−FFv−FFe with 4-conditionally faulty, as follows: (1) For n≥3, FQn−FFv−FFe contains a fault-free cycle of every even length from 4 to 2n−2|FFv|, where |FFn|+|FFe| ≤ 2n−5; (2) For even n≥4, FQn−FFv−FFe contains a fault-free cycle of every odd length from n+1 to 2n−2|FFv|−1, where |FFv|+|FFe| ≤ 2n−5.
Liberal arts academia wants YOU!
Authors: Davis Janet 
Published: January 2017

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

twitter

Follow us on Twitter at http://twitter.com/blogCACM
http://cacm.acm.org/blogs/blog-cacm
Janet Davis makes a plea to CS practitioners to consider even a short teaching stint.