bluuebunny/crossref_metadata_2025 huggingface dataset:
Differences in pollination success between local and foreign flower color phenotypes: a translocation experiment with Gentiana lutea (Gentianaceae)
Authors: Guitián Javier A , Sobral Mar , Veiga Tania , Losada María , Guitián Pablo , Guitián José M
Published: January 2018

Background. The adaptive maintenance of flower color variation is frequently attributed to pollinators in part because they preferentially visit certain flower phenotypes. We test whether Gentiana lutea – which shows a flower color variation (from orange to yellow) in the Cantabrian Mountains range (north of Spain) − is locally adapted to the pollinator community.

Methods. We transplant orange-flowering individuals to a population with yellow-flowering individuals and vice-versa, to assess whether there is a pollination advantage in the local morph comparing its visitation rate with the foreign morph.

Results. Our reciprocal transplant experiment showed no clear signal of local morph advantage at one site; thus, there is no evidence of local adaptation in Gentiana lutea to the pollinator assemblage. However, some floral visitor groups (such as Bombus pratorum, B. soroensis ancaricus and B. lapidarius decipiens) consistently preferred the local morph to the foreign morph whereas others (such as Bombus terrestris) consistently preferred the foreign morph.

Discussion. We concluded that there is no evidence of local adaptation to the pollinator community in each of the two G. lutea populations studied. The consequences for local adaptation to pollinator on G. lutea flower color would depend on the variation along the Cantabrian Mountains range in morph frequency and pollinator community composition.
How diverse is your team? Investigating gender and nationality diversity in GitHub teams
Authors: Ortu Marco , Destefanis Giuseppe , Counsell Steve , Swift Stephen , Marchesi Michele , Tonelli Roberto
Published: January 2018

Building an effective team of developers is a complex task faced by both software companies and open source communities. The problem of forming a “dream” team involves many variables, including consideration of human factors, and it is not a dilemma solvable in a mathematical way. Empirical studies might provide interesting insights to explain which factors need to be taken into account in building a team of developers and which levers act to optimise collaboration and productivity among developers. In this paper, we present the results of an empirical study aimed at investigating the link between team diver- sity (i.e., gender, nationality) and productivity (issue fixing time). We consider issues solved from the GHTorrent dataset inferring gender and nationality of each team’s members. We also evaluate the politeness of all comments involved in issue resolution. Results show that higher gender diversity is linked with a lower team average issue fixing time and that nationality diversity is linked with lower team politeness.
Potential ecosystem services of urban agriculture: a review
Authors: Aerts Raf , Dewaelheyns Valerie , Achten Wouter MJ
Published: January 2018

Urban agriculture (UA) is increasingly proposed as an environmentally friendly answer to global challenges including urbanization, public health, food security and climate change. We provide an overview of present evidence of ecosystem services delivered by UA that could potentially increase the sustainability of the urban ecosystem, including the often claimed reduced greenhouse gas emissions. There is general agreement that UA is important for local food production, especially in the south; that UA has a role in regulating green and blue water flows, organic waste flows and pollination; and that UA has important socio-cultural values, including an improved quality of city life and increased local community capacity. There is some evidence that UA may also improve human health because of dietary changes in certain social classes, but these are potentially confounded by environmental pollution in the city. Quantitative evidence is very limited for all ecosystem services, but the available data nevertheless suggests that the overall food productivity and the total reductions in greenhouse gas emission are low at global or city-wide scale despite the fact that UA has potential strong effects on food security at the local scale. The current eagerness of industrialized cities to integrate UA into their food policies as an approach to become “climate neutral” or to rely on ecosystem services to become more resilient calls for life cycle assessment studies that accurately quantify emission reductions and other urban ecosystem services of urban agriculture.
Diversity is the question, not the answer
Authors: Shade Ashley
Published: January 2018

Local (within-sample/alpha) diversity is often implicated as a cause of success or failure of a microbial community. However, the relationships between diversity and emergent properties of a community, such as its stability, productivity, or invasibility, are much more nuanced. In the submitted manuscript, I argue that diversity without context provides limited insights into the mechanisms underpinning community patterns. I provide examples from traditional and microbial ecology to discuss common complications and assumptions about within-sample diversity that may prevent us from digging deeper into the more specific mechanisms underpinning community outcomes. I suggest that measurement of diversity should serve as a starting point for further inquiry of ecological mechanisms rather than an “answer” to community outcomes.
Development of a WEB-GIS real-time dynamic landslide risk scenarios procedure – Umbria Region civil protection early warning system, a case study
Authors: Ponziani Francesco , Stelluti Marco , Berni Nicola
Published: January 2018

Umbria Region Functional Centre, part of the Umbria Region Civil Protection Dept., since 2009 has developed an experimental, operational early warning system for landslide risk assessment, based on rainfall thresholds, soil moisture evaluation, quantitative precipitation forecasts – QPF, and an open source WebGIS decision support subsystem/platform – DSS. Rainfall thresholds were obtained by the analysis of past landslide events, correlated with their initial soil moisture condition reconstruction: observed and forecasted accumulated rain, together with modeled saturation index, compared with threshold values at different alert levels, lead to the production of early warning indicators, calculated at each point of a 738 grid covering the entire Umbria Region. The evaluation of the indicator grid values, is used on a daily base for the alerting state assessment over the regional territory; but, in order to take full advantage of all the available information layers useful for the hydrogeological risk evaluation, a real time scenario with high spatial resolution was developed too: every time that second-level rainfall thresholds are exceeded, the early warning indicators are used to start a procedure aimed at dynamic, real time risk scenario generation. A Linux API “inotify” waits for changes on warning indicators-thresholds ratio: if overtopping conditions are reached, the risk scenario procedure initiate a “bash” Linux script with all the commands aimed at generating and inserting the resulting geotiff on the web-gis platform. Aimed to the generation of the risk scenario, Geospatial Data Abstraction Library (gdal library) composed by raster and vector utility programs, calculating risk from hazard, susceptibility and vulnerability layers is used. More in detail, a procedure has been developed as follows: Step #1: from early warning indicators (hazard information), a dense interpolated regular grid using inverse distant weight algorithm is used; Step #2: in order to combine time-dependent landslide hazard with space-dependent landslide susceptibility, different types of susceptibility layers are used; final step: Exposed elements/vulnerability information (buildings, infrastructures, etc...) is used, able of leading to the generation of a dynamic, real-time risk scenario. Using the “gdal_calc.py” program, raster combined data produce the risk scenario layer. Then, real-time results are published on the web-gis platform. General performances appear to be promising and satisfactory for Civil Protection purposes (alerting issues, emergency management, territorial presidium/direct monitoring of the territory organization, etc..). Open source Web – GIS platforms appear to be an ideal tool in order to share dynamic hazard/risk scenarios with all the institutional subjects and stakeholders involved, and allow administrations to maintain sustainable and flexible operational systems.
Enhancing fisheries education in Canada: The need for interdisciplinarity, collaboration, and inclusivity
Authors: Turgeon Katrine , Hawkshaw Sarah C.F. , Dinning Kristin M. , Quinn Brady K. , Edwards Danielle N. , Wor Catarina , Parlee Courtenay E. , Debertin Allan , Hawkshaw Mike , Nelson Benjamin W. , Zhang Fan , Benestan Laura M , Angel Eric , Morse Bryan L. , Mombourquette Daniel
Published: January 2018

The Canadian Fisheries Research Network (CFRN) was initiated to increase interdisciplinary research capacity through enhanced, cross-sector collaboration. Training in the CFRN was important and unique for students because of the exposure to the realities of industry, government and academics working in close collaboration. As CFRN students, our goal for this paper was to assess whether Canada is appropriately preparing the next generation of fisheries graduates to tackle complex fisheries management problems. This assessment consisted of 1) a systematic review of fisheries-related education across Canada, 2) a reflection on our experience in the CFRN, and 3) comments on the importance of inclusive and interdisciplinary approaches in fisheries education and fisheries research. Based on our assessment, we concluded that the availability of fisheries education in Canada is limited, particularly with respect to interdisciplinary training. We contend that the CFRN enhanced our educational experience by fostering interdisciplinary and inclusive fisheries research. We recommend that the CFRN model be considered both in the development of fisheries education initiatives and in the design of future fisheries research.
Cockatiel (Nymphicus hollandicus) gut microbiomes, bacterial inhabitants of a worldwide distributed pet
Authors: Alcaraz Luis David , Hernández Apolinar M. , Peimbert Mariana
Published: January 2018

Background. Cockatiels (Nymphicus hollandicus) were originally endemic to Australia, but they are nowadays popular worldwide pet birds. It is now possible to make detailed molecular studies on cultivable and uncultivable bacteria that are part of the intestinal microbiome of healthy animals, these studies showed that bacteria are an essential part of the capacity and metabolic status of animals. There are few studies of bird microbiomes and to date this is the first reported cockatiel microbiome work. Methods. In this paper we analyzed the gut microbiome of 3 healthy adult cockatiel birds by massive sequencing of 16S ribosomal gene. Additionally, we show a comparison with other poultry, and wild birds microbiomes and their taxa profiles Results. The vast majority of the Cockatiel’s bacteria found were Firmicutes, while Proteobacteria and Bacteroidetes are poorly represented. 19,280 different OTUs were detected, of which 8,072 belong to the Erysipelotrichaceae family. Discussion. Cockatiels wide geographic distribution, and close human contact makes relevant to study their microbiomes, this study gives a baseline for their bacterial diversity. Cockatiels microbiomes diversity are dominated by Firmicutes of the Erysipelotrichaceae family. Cockatiels, and other wild birds are almost depleted of Bacteroidetes which happen to be abundant in poultry birds and this is probably related with the intensive human manipulation of poultry bird diets. Some pathogenic bacteria like Clostridium colinum, and Serratia marcescens are inhabitants of the cockatiel’s microbiome while other pathogens are not elements of healthy cockatiel’s microbiota, although the specimens collected were perfectly healthy at the time.
Knockout Sudoku, a method for rapidly curating gene disruption collections
Authors: Anzai Isao A , Shaket Lev , Adesina Oluwakemi , Baym Michael , Barstow Buz
Published: January 2018

Knockout Sudoku is a method for the construction of whole-genome knockout collections for a wide range of microorganisms with as little as 3 weeks of dedicated labor and at a cost of approximately $10,000. The method uses manual 4-dimensional combinatorial pooling, next-generation sequencing and a Bayesian inference algorithm to rapidly process and then accurately annotate the extremely large progenitor transposon insertion mutant collections needed to achieve saturating coverage of complex microbial genomes. Here we present a protocol for the generation, combinatorial pooling and annotation of highly oversampled progenitor collections and their subsequent algorithmically guided condensation and curation into high-quality collections suitable for rapid genetic screening and gene discovery.
Fetus-in-fetu in an 8-month-old girl
Authors: Zhao Bei Bei , Bai Yu Zuo
Published: January 2018

Fetus in fetu (FIF) is a very rare congenital malformation with an incidence of 1/500,000 live births. These children are often hospitalized because of vomiting, abdominal distension or abdominal mass found by their parents. The most common position for the parasitic fetus is the retroperitoneum but other position such as the scrotal sac, cranial cavity, sacrococcygeal region, back , oral cavity has been reported. FIF is often misdiagnosed as a mature teratoma. Ultrasound, CT, MRI are of great significance in distinguishing between FIF and teratoma. The postoperative pathological examination may reveal axial skeleton which can make a definitive diagnosis of FIF. In this report, we present a case of FIF in an 8-month-old girl.
TwitterNews: Real time event detection from the Twitter data stream
Authors: Hasan Mahmud , Orgun Mehmet A , Schwitter Rolf
Published: January 2018

Research in event detection from the Twitter streaming data has been gaining momentum in the last couple of years. Although such data is noisy and often contains misleading information, Twitter can be a rich source of information if harnessed properly. In this paper, we propose a scalable event detection system, TwitterNews, to detect and track newsworthy events in real time from Twitter. TwitterNews provides a novel approach, by combining random indexing based term vector model with locality sensitive hashing, that aids in performing incremental clustering of tweets related to various events within a fixed time. TwitterNews also incorporates an effective strategy to deal with the cluster fragmentation issue prevalent in incremental clustering. The set of candidate events generated by TwitterNews are then filtered, to report the newsworthy events along with an automatically selected representative tweet from each event cluster. Finally, we evaluate the effectiveness of TwitterNews, in terms of the recall and the precision, using a publicly available corpus.
S-phase kinase-associated protein 2 positively controls mitotic arrest deficient 2 in lung cancer cells
Authors: Huang Tonghai , Yang Lin , Wang Guangsuo , Ding Guanggui , Peng Bin , Wen Yuxin , Wang Zheng
Published: January 2018

Background. Mitotic arrest deficient 2 (Mad2) is a key component of spindle assembly checkpoint and overexpressed in human lung cancers, but the mechanism of the deregulation of Mad2 in lung cancer is largely unknown. We aim to investigate the regulation of Mad2 by S-phase kinase-associated protein 2 (Skp2) in human lung cancer cells.

Methods. Human lung cancer A549 and NCI-H1975 cells were transfected with MAD2 and SKP2 siRNAs or plasmids to silence or overexpress MAD2 and SKP2. Flavopiridol and HLM006474 were used to inhibit cyclin dependent kinases (CDKs) and E2F1, respectively. mRNA and protein levels were determined by real-time PCR and Western blot, respectively. Cell cycle progression was assayed by flow cytometery.

Results. Knockdown of Skp2 by siRNA decreased Mad2 mRNA and protein levels in A549 and NCI-H1299 cells, accompanied with upregulation of p27 but decrease of the phosphorylation of retinoblastoma (Rb). In contrast, ectopic overexpression of Skp2 increased Mad2 mRNA and protein levels and phosphorylation of Rb, while decreased p27. Pharmacological inhibition of CDK1/2 by flavopiridol or E2F1 with HLM006474 led to downregulation of Mad2 expression, and prevented the increase of Mad2 expression by Skp2. Accordingly, silencing of either Mad2 or Skp2 impaired the mitosis arrest in response to nocadazole.

Conclusion. SKP2 positively regulates the gene expression of MAD2 through p27-CDKs-E2F1 signaling pathway, suggesting that deregulation of Skp2 may lead to upregulation of Mad2 via enhancing the activity of CDKs in human lung cancers. Our findings may provide an explanation of the simultaneous upregulation of MAD2 and SKP2 in lung cancer and potential targets for the development of molecular targeted therapy for lung cancers.
Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork
Authors: Yahara Koji , Méric Guillaume , Taylor Aidan J , de Vries Stefan PW , Murray Susan , Pascoe Ben , Mageiros Leonardos , Torralbo Alicia , Vidal Ana , Ridley Anne M , Komukai Sho , Wimalarathna Helen , Cody Alison J , Colles Frances M , McCarthy Noel D , Harris David , Bray James E , Jolley Keith A , Maiden Martin CJ , Bentley Stephen D , Parkhill Julian , Bayliss Christopher D , Grant Andrew J , Maskell Duncan , Didelot Xavier , Kelly David J , Sheppard Samuel K
Published: January 2018

Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7,343 MLST-characterised isolates, we sequenced 600 C. jejuni and C. coli isolates from various stages of poultry processing and clinical cases. A genome-wide association study (GWAS) in C. jejuni ST-21 and ST-45 complexes identified genetic elements over-represented in clinical isolates that increased in frequency throughout the poultry processing chain. Disease-associated SNPs were distinct in these complexes, sometimes organised in haplotype blocks. The function of genes containing associated elements was investigated, demonstrating roles for cj1377c in formate metabolism, nuoK in aerobic survival and oxidative respiration, and cj1368-70 in nucleotide salvage. This work demonstrates the utility of GWAS for investigating transmission in natural zoonotic pathogen populations and provides evidence that major C. jejuni lineages have distinct genotypes associated with survival, within the host specific niche, from farm to fork.
Effect of stratiﬁcation and gibberellic acid on epicotyl dormancy release in seeds of Yunnanopilia longistaminea (Opiliaceae)
Authors: Yang Guan-song , Yang Liu , Wang Yue-hua , Shen Shi-kang
Published: January 2018

Yunnanopilia longistaminea is an endangered monotypic species belonging to Opiliaceae. This edible plant is an important germplasm source with a high economic value in China. The seed dormancy and germination of Opiliaceae species have been rarely investigated. This study examined the effects of scarification, soaking in gibberellic acid, and dehydration on the seed germination of Y. longistaminea. Results indicated that the seed germination of this species involves two stages: radicle emergence and epicotyls (shoot) emergence. During radicle emergence, the optimum temperatures were 28 °C and 28 °C/20 °C. Seed moisture content and viability decreased as dehydration occurred. Thus, the seeds may be recalcitrant. The optimum GA3 solution for the seeds undergoing shoot emergence was 100 mg·L−1. The percentages of shoot emergence in 7 and 14 days of stratiﬁcation at 5 °C were slightly higher than those in other groups. This study is the first to describe epicotyl dormancy in Y. longistaminea seeds. From the seed grow to the seedling of Y. longistaminea subjected to a autumn→winter→spring temperature process in nature conditions. Warm and cold stratiﬁcation can alleviate radicle and epicotyl dormancy, respectively. The duration of cold stratiﬁcation also significantly affects the epicotyl dormancy release of Y. longistaminea. The researches on the seeds breaking methods: warm(28°C/20°C)→cold(5°C)→GA3(100mg·L−1)→warm(28°C/20°C).
Seasonal changes in fish assemblage structure at a shallow seamount in the Gulf of California
Authors: Jorgensen Salvador J , Klimley A. Peter , Muhlia-Melo Arturo , Morgan Steven G
Published: January 2018

Seamounts have generally been identified as locations that can promote elevated productivity, biomass and predator biodiversity. These properties attract seamount-associated fisheries where elevated harvests can be obtained relative to surrounding areas. There exists large variation in the geological and oceanographic environment among the thousands of locations that fall within the broad definition of seamount. Global seamount surveys have revealed that not all seamounts are hotspots of biodiversity, and there remains a strong need to understand the mechanisms that underlie variation in species richness observed. We examined the process of fish species assembly at El Bajo Espiritu Santo (EBES) seamount in the Gulf of California over a five-year study period. To effectively quantify the relative abundance of fast-moving and schooling fishes in a ‘blue water’ habitat, we developed a simplified underwater visual census (UVC) methodology and analysis framework suitable for this setting and applicable to future studies in similar environments. We found correlations between seasonally changing community structure and variability in oceanographic conditions. Individual species responses to thermal habitat at EBES revealed three distinct assemblages, a ‘summer assemblage’ tracking warmer overall temperature, a ‘winter assemblage’ correlated with cooler temperature, and a ‘year-round assemblage’ with no significant response to temperature. Species richness was greatest in spring, when cool and warm water masses stratified the water column and a greater number of species from all three assemblages co-occurred. We discuss our findings in the context of potential mechanisms that could account for predator biodiversity at shallow seamounts.
Chimpanzee energetics, ecology, and evolution
Authors: Pontzer Herman , Brown Mary H. , Emery Thompson Melissa , Ross Stephen R.
Published: January 2018

Chimpanzees have the largest relative brain size, greatest reproductive output, and longest lifespan of any non-human ape; they also have the highest level of physical activity in the wild, as measured by daily walking and climbing distances. In this study, we examined variation in total energy expenditure (TEE, kcal/day), body composition, oxidative stress, and physical activity to test whether chimpanzees have evolved metabolic strategies to fuel these evolved changes in ecology, encephalization, and life history. We used the doubly labeled water method to measure TEE and body fat percentage in adult chimpanzees (Pan troglodytes, n=27), bonobos (Pan paniscus, n=8), Western lowland gorillas (Gorilla gorilla, n=10), and orangutans (Pongo spp., n=11) housed in zoos and sanctuaries. Walking and climbing activity was recorded via direct observation. Oxidative stress was assayed via urinary 8-hydroxy-2' -deoxyguanosine (8-OHdG). Chimpanzee metabolic and activity measures were similar to bonobos’ (p>0.05 all comparisons). In comparisons among genera, TEE in Pan was greater than that of Pongo (p<0.01) and trended higher than that of Gorilla (p=0.22) in multiple regression controlling for body size and activity. By contrast, urinary 8-OHdG and percent body fat were lower in Pan than in Gorilla or Pongo (p<0.05) in analyses controlling for age. These results indicate that chimpanzees have evolved an accelerated metabolism while simultaneously decreasing the safety margin against food shortage that body fat provides. We discuss this metabolic acceleration, which appears to predate the chimpanzee-bonobo divergence, and its importance for reconstructing the ecological pressures shaping chimpanzee life history, anatomy, and ranging.
Redescription of Arundel formation Ornithomimosaur material and a reinterpretation of Nedcolbertia justinhofmanni as an “Ostrich Dinosaur”: Biogeographic implications
Authors: Brownstein Chase Doran
Published: January 2018

The fossil record of dinosaurs from the Early Cretaceous of eastern North America is scant, especially since few formations from the east are fossiliferous. Among those that are is the Arundel Formation of the eastern seaboard, which has produced among the best dinosaur faunas known from the Early Cretaceous of eastern North America. The diverse dinosaur fauna of this formation has been thoroughly discussed previously, but few of the dinosaur species originally described from the Arundel are still regarded as valid genera. Much of the Arundel material is in need of review and redescription. Among the fossils of dinosaurs from this formation are those referred to ornithomimosaurs. Here, I redescribe ornithomimosaur remains from the Arundel facies of Prince George’s County, Maryland which may be from two distinct ornithomimosaur taxa. These remains provide key information on the theropods of the Early Cretaceous of Eastern North America. Recent discoveries of small theropod material from the Arundel Formation are also reviewed and described for the first time. The description of the Arundel material herein along with recent discoveries of basal ornithomimosaurs in the past 15 years has allowed for comparisons with the coelurosaur Nedcolbertia justinhofmanni, suggesting the latter animal was a basal ornithomimosaurian dinosaur rather than a “generalized” coelurosaur as which it was originally described. Comparisons between the Arundel ornithomimosaur material and similar Asian and European specimens suggest that both extremely basal ornithomimosaurs and more intermediate or derived forms coexisted throughout the northern hemisphere during the Early Cretaceous. Additionally, the possible presence of two distinct ornithomimosaurs in the Arundel allies the Arundel facies with Asian sediments in their coelurosaurian fauna.
African meliponine bees (Hymenoptera: Apidae) maintained in man-made hives as potential hosts for the small hive beetle, Aethina tumida Murray (Coleoptera: Nitidulidae)
Authors: Bobadoye Bridget O , Ayuka Fombong T. , Kiatoko Nkoba , Raina Suresh , Teal Peter , Torto Baldwyn
Published: January 2018

Previous studies have shown that natural honeybee and bumble bee colonies are hosts of the small hive beetle (SHB) Aethina tumida, a pest of honeybee colonies in various regions of the world. Recent studies also reported the presence of SHBs in colonies of certain meliponine bee species. In this study, we investigated whether SHBs detect odors of African meliponine bees and their hive matrix components. We also compared the chemical profiles of the honeybee Apis mellifera scutellata and meliponine bee odors in order to identify common potential semiochemicals between the two bee species. We used dual-choice olfactometric assays to test the responses of adult male and female SHBs to intact colony odors from six meliponine bee species, namely Hypotrigona gribodoi, Meliponula ferruginea (black), M. ferruginea (reddish-brown), Plebeina hildbrandti, M. bocandei and M. lendiliana and their hive matrix components including pot honey, pot pollen, cerumen (involucrum) and propolis (batumen). We found that female SHBs responded more strongly to odors from intact colonies, pot honey and pollen from five out of the six species tested than male beetles. Chemical analysis identified several common components in colony odors emitted by both honeybees and a representative meliponine bee species, M. ferruginea (black). In particular, nine of these common components previously have been shown in honeybee volatiles to be semiochemicals for the SHB, suggesting that African meliponine bees can also serve as potential alternate hosts for the beetle. The implications of these results are discussed in the context of domesticating African meliponine bees in man-made hives for the pollination of crops.
Diverse origins of high copy tandem repeats in grass genomes
Authors: Bilinski Paul , Han Yonghua , Hufford Matthew B , Lorant Anne , Zhang Pingdong , Jiang Jiming , Ross-Ibarra Jeffrey
Published: January 2018

In studying genomic architecture, highly repetitive regions have historically posed a challenge when investigating sequence variation and content. High-throughput sequencing has enabled researchers to use whole-genome shotgun sequencing to estimate the abundance of repetitive sequence, and these methodologies have been recently applied to centromeres. Here, we utilize sequence assembly and read mapping to identify and quantify the genomic abundance of different tandem repeat sequences. Previous research has posited that the highest abundance tandem repeat in eukaryotic genomes is often the centromeric repeat, and we pair our bioinformatic pipeline with fluorescent in-situ hybridization data to test this hypothesis. We find that de novo assembly and bioinformatic filters can successfully identify repeats with homology to known tandem repeats. Fluorescent in-situ hybridization, however, shows that de novo assembly fails to identify novel centromeric repeats, instead identifying other potentially important repetitive sequences. Together, our results test the applicability and limitations of using de novo repeat assembly of tandem repeats to identify novel centromeric repeats. Building on our findings of genomic composition, we also set forth a method for exploring the repetitive regions of non-model genomes whose diversity limits the applicability of established genetic resources.
Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy
Authors: Brazelton William J , Thornton Christopher N , Hyer Alex , Twing Katrina I , Longino August A , Lang Susan Q , Lilley Marvin D , Früh-Green Gretchen L , Schrenk Matthew O
Published: January 2018

The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.
Live cell imaging of Salmonella Typhimurium interaction with zebrafish larvae after injection and immersion delivery methods
Authors: Varas Macarena A , Fariña Alonso , Díaz-Pascual Francisco , Ortíz-Severín Javiera , Marcoleta Andrés E , Allende Miguel L , Santiviago Carlos A , Chávez Francisco P
Published: January 2018

Surrogate host models have been employed to study bacterial virulence mechanisms of important human pathogens. Particularly, zebrafish (Danio rerio) has been used to determine the role of vertebrate innate immunity during bacterial infections. The easy-to-obtain large number of embryos and optical transparency of larvae allow live cell imaging of the infection progress and the major cellular types of the innate immune system that develop during the first days of embryogenesis. In zebrafish model, microinjecting bacteria into embryos and/or larvae can cause infection. Alternatively, an infection can be generated by static immersion of larvae on a microbial suspension. Both methods differ in the mode and time of infection, inoculum size and host response. In this work, we compare the in vivo immune response induced by Salmonella enterica serovar Typhimurium (S. Typhimurium) inoculated by immersion and microinjection in zebrafish larvae. To this end, an immersion protocol using transgenic zebrafish larvae was developed for in vivo monitoring of GFP-tagged S. Typhimurium infection progress and immune response during 72 h. The infection progress was compared to that of zebrafish larvae inoculated by microinjection. Our results in zebrafish corroborate previous Salmonella virulence studies in murine models and reveal that host-pathogen interaction not only depends on the virulence of the strain, but also on the inoculation method and host conditions.
The correlation of climate factors on dengue transmission in urban area: Bangkok and Singapore cases
Authors: Polwiang Sittisede
Published: January 2018

The objective of this study is to find the correlation between climate factors and dengue incidence rate in Bangkok and Singapore during 2009-2015. Spearman's rank correlation tests with time-lag are performed to investigate the overall correlation between dengue incidence rates and climate factors , minimum, mean, and maximum temperatures, DTR, and rainfall. A Linear and Poisson regression analysis was performed. Spearman's rank correlation tests show that in Bangkok monthly rainfall (r=0.451, p<0.001), the number of rainy days (r=0.411, p<0.001) are positive correlation with 2 month lag time. DTR (r=-0.335, p<0.001) is negative correlation with 2 month lag time. Maximum (r=0.256, p<0.001), mean (r=0.304, p<0.001) and minimum (r=0.323, p<0.001) temperature are positive correlation with 4 month lag time. In Singapore, only minimum temperature (r=-0.299, p<0.001) with 1 month lag time is negative correlation and DTR (r=-0.289, p<0.001) with zero month lag time is positive correlation. The rest has no statically significance (p>0.05). This study concluded, climate factors play moderate role in dengue incidence in Bangkok. There is no statistical significance between rainfall and dengue incidence rate and temperature play a marginal role in Singapore.
Phalangeal joints kinematics during Ostrich (Struthio Camelus) locomotion
Authors: Zhang Rui , Ji Qiaoli , Luo Gang , Xue Shuliang , Ma Songsong , Li Jianqiao , Ren Lei
Published: January 2018

The ostrich is a highly cursorial bipedal land animal with a permanently elevated metatarsophalangeal joint supported by only two toes. Although locomotor kinematics in walking and running ostriches have been examined, these studies have been largely limited to above the metatarsophalangeal joint. In this study, kinematic data of all major toe joints were collected from walking to running during stance period in a semi-natural setup with selected cooperative ostriches. Statistical analyses were conducted to investigate the effect of locomotor gait on toe joint kinematics. The MTP3 and MTP4 joints exhibit the largest range of motion whereas the first phalangeal joint of the 4th toe shows the largest motion variability. The interphalangeal joints of the 3rd and 4th toes present very similar motion patterns over stance phases of walking and running. However, the motion patterns of the MTP3 and MTP4 joints and the vertical displacement of the metatarsophalangeal joint are significantly different during running from walking. This is probably because of the biomechanical requirements for the inverted pendulum gait at low speeds and also the bouncing gait at high speeds. Interestingly, the motions of the MTP3 and MTP4 joints are highly synchronised from slow to fast locomotion. This strongly suggests that the 3rd and 4th toes really work as an integrated system with the 3rd toe as the main load bearing element whilst the 4th toe as the complementary load sharing element with a primary role to ensure the lateral stability of the permanently elevated metatarsophalangeal joint.
A new specimen-dependent method of estimating felid body mass
Authors: Sherani Shaheer
Published: January 2018

Background. The estimation of body mass of long extinct species of the family Felidae has been a focus of paleontology. However, most utilized methods impose expected proportions on the fossil specimens being estimated, resulting in a high chance of underestimation or overestimation. This study proposes a new method of estimating felid body mass by accounting for osteological proportionality differences between the extinct taxa being estimated and the living species being used as comparisons.

Method. Using a manipulation of the cube law, 36 equations were formulated that estimate body mass based on certain humeral and femoral dimensions. The formulated equations were used to examine whether the mass of living comparison species, namely the tiger (Panthera tigris), the lion (Panthera leo), and the jaguar (Panthera onca), depends equally on a select set of long bone dimensions. The body mass of five extinct felids, namely Panthera atrox, Panthera spelaea, Panthera tigris soloensis, Smilodon populator, and Smilodon fatalis, was also estimated.

Results. Living comparisons species were found to somewhat incorrectly estimate other living comparison species. All five extinct taxa were found to weigh well over 300 kg, with the largest of the species weighing nearly 500 kg.

Discussion. The inability of one living comparison species to predict the mass of another with strong accuracy suggests that bone dimensions do not solely influence body mass. Discrepancies between the masses of Smilodon populator and Smilodon fatalis were likely the product of the difference in available niches in late Pleistocene North and South America. The masses of Panthera spelaea and Panthera atrox indicate a discrepancy in sociality between the two closely related species. Lastly, the extreme body mass of Panthera tigris soloensis points to great plasticity within the tiger lineage in terms of size, indicating that such variations among tiger populations may not warrant subspeciation.
Promotion of surface energy closure by monitoring tree biomass heat storage
Authors: Yu Minghan , Ding Guodong , Gao Guanglei , Zhao Yuanyuan , Sai Ke , Li Xu , Wang Yue , Liu Yundong
Published: January 2018

Biomass heat storage is important for promoting energy closure in forest ecosystems; however, this issue is often ignored in surface energy budgets. To determine an accurate approach to calculate biomass heat storage, we monitored the stem temperature of Pinus sylvestris in different heights, depths and orientations. At the same time, air sensible and latent heat storage and soil heat storage are also monitored together with biomass heat storage to study the heat storage share in surface energy budgets. The results showed that (1) temperature in different heights, depths and orientations in stem showed obviously differences dynamics, and time lags are existed between different measuring points inside stem. (2) Tree biomass heat flux varied around 12 W m−2. Soil heat flux and air heat storage were around 20 W m−2 and 8 W m−2 separately, but out of phase with biomass heat flux. (3) Total heat storage in soil, biomass, and air was 60 W m −2 , accounting for ~10% of net radiation, which is a significant proportion of the total energy flux. This study will help improve biomass heat storage models and contribute to fundamental knowledge regarding energy balance closure in forest ecosystems.
Augmenting caregiver in-home safety practices via mHealth: A randomized controlled trial
Authors: L. Wilson Michael , Kigwangalla Hamisi A.
Published: January 2018

Unintentional injuries among under-fives represent an important cause of preventable morbidity in Dar es Salaam, Tanzania. In-home interventions targeting caregiver safety practices currently show promise in reducing household injury risks. Mobile health (mHealth) is emerging as a potentially cost effective platform for the delivery of critical health information in resource poor settings. The goal of this project is to introduce an mHealth intervention targeting household risk factors for child burn injuries in Dar es Salaam.
Empirical assessment of transgene flow from transgenic poplar plantation
Authors: Hu Jianjun , Zhang Jin , Chen Xingling , Lv Jinhui , Jia Huixia , Zhao Shutang , Lu Mengzhu
Published: January 2018

To assess the possible impact of transgenic poplar plantations on the ecosystem, we analyzed the frequency and distance of gene flow from a mature male transgenic Populus nigra carried Bacillus thuringiensis toxin gene (Bt-OE poplar) plantation, and the survival of Bt-OE poplar seeds as well. The resultant Bt-OE poplar seeds occurred at a frequency from ~0.15% at 0 m to ~0.02% at 500 m far away from the Bt-OE poplar. The Bt-OE poplar seeds weaken and even lost germinated activation within 3 weeks in the field (from 68% to 0%), compared to the 48% germination rate after 3 weeks in 4°C. The survival rate of seedlings in the field is 0% without any treatments, but increased to 1.7% under four treatments (Clean and trim, watering, weeding, and cover with plastic to keep moisture) together after seeded in the field for eight weeks. Results of this study indicate that gene flow originated from Bt-OE poplar plantation through pollen and seed could happen at a very low rate and in a limited range in natural conditions. This study provide the first-hand field data on the extent of transgene flow in poplar plantations, and offer guidance for risk assessment of transgenic poplar plantations.
Bovine tuberculosis in cattle from 1986 to 2012 in and around badger-culled areas of the RBCT
Authors: Hendy David
Published: January 2018

In 2007 the Independent Scientific Group (ISG) reported to the UK government the impact on bovine tuberculosis (TB) in cattle of a trial where badgers were culled between 1998 and 2005. This trial, known as the Randomised Badger Culling Trial (RBCT), was performed across 100 km2 (nominal) zones in the West of England. The results were based on a model of new herd incidence data. It was concluded that reactive culling generated overall detrimental effects, while proactive culling achieved very modest overall benefits at the cost of elevated incidence on neighbouring farms.

This work looks at more extensive RBCT data to examine if these findings hold true. Instead of presenting the results of a model, this work directly illustrates data supplied in March 2016 by the Animal and Plant Health Agency. Such data covers a greater number of years (1986 to 2012) and includes the prevalence of herd restrictions as well as herd incidence.

It appears that whilst cattle TB noticeably reduced in areas subjected to proactive culling, TB did not significantly increase in the surrounding areas. The more limited reactive culls were found to have no significant impact either positively or negatively. This applied to both the treated and surrounding areas.

The more extensive data also showed that culling badgers only reduced confirmed TB with no significant impact on unconfirmed TB. This was also found by the ISG in 2007 when using their model.

The delay before culling benefit became apparent was about 5 years after the first substantial cull. This has implications for the culls which started in South West England in 2013. If account is taken for the need to average the data, the number of years needed to see TB drop, and the reporting delay, it may not be until September 2023 before the impact of these culls become clear. Also, if culls stop after year four in each zone, this risks benefits falling short of those achieved in the RBCT.
Randomised Badger Culling Trial: Impact, based on more extensive data
Authors: Hendy David
Published: January 2018

In 2007 the Independent Scientific Group (ISG) reported to the UK government the impact on bovine tuberculosis (TB) in cattle of the Randomised Badger Culling Trial (RBCT). Badgers were culled between 1998 and 2005 across 100 km2 (nominal) zones in the West of England. The results were based on a model of New Herd Incidence (NHI). It was concluded that reactive culling generated overall detrimental effects, while proactive culling achieved very modest overall benefits at the cost of elevated incidence in surrounding areas.

This work looks at more extensive RBCT data to examine if these findings hold true. Instead of presenting the results of a model, this work directly illustrates the data. The Animal and Plant Health Agency supplied this data in March 2016. Such data covers a greater number of years (1986 to 2012) and includes the prevalence of herd restrictions as well as herd incidence.

Whilst the proactive culls substantially and sustainably reduced cattle TB in treated areas, such culls did not significantly increase TB in the surrounding areas. In fact NHIs between 2006 and 2012 dropped by 28%, 1% and 18% in the treated, outer 2km ring, and combined areas respectively. Based on the number of NHIs prevented since 1998, a break-even cost to complete a badger removal exercise was calculated to be £8,693 per km2. This figure may be under-estimated because it takes no account of any NHIs prevented after 2012.

The more limited reactive culls had no impact on both the treated area and outer 2km ring. Proactive culling only reduced confirmed TB with no significant impact on unconfirmed TB.

Conclusions in the RBCT Final Report, which were based on the results of a model of time-shifted early data, poorly reflect the greater benefits seen in this more extensive data. Badger culling is highly contentious in the UK and many press reports adversely report the effectiveness of badger culling in general and the culls which started in 2013 in particular. Unfortunately the RBCT conclusions are often cited to add credence to these press reports. In the RBCT, after the first year of substantial culling, this work found that 9 years of data were needed to clearly see the full extent by which TB dropped when plotted against calendar year. The impact of the culls, which started in late 2013, may not become clear until late 2023 after a 2-year reporting delay.

This work was restricted to looking at data showing total TB breakdowns over all triplets. Further work to examine breakdowns by triplet or groups of triplets should reveal more.
A non-destructive technique for chemical mapping of insect inclusions in amber
Authors: Popovski Kolaceke Anezka , McKellar Ryan C , Barbi Mauricio
Published: January 2018

Synchrotron-based techniques offer a wealth of elemental, molecular, and structural insights in biological samples, but the application of these techniques to fossils is a relatively new development. Here we examine how Synchrotron Radiation Micro X-Ray Fluorescence (SR µXRF) provides insights into the chemical composition of insects trapped in amber, while leaving the inclusions unaltered. By analyzing a series of ants (Hymenoptera: Formicidae) that range from modern material, to Eocene Baltic amber, and Late Cretaceous North Carolina amber, we investigate how variable preservation influences the results obtained through SR µXRF analyses, as well as the various merits and pitfalls associated with the application of this technique to amber inclusions. The initial results from this line of research are encouraging. They provide new avenues to study elements that are original to the specimens involved, as well as those generated through decay, or introduced during taphonomic processes. This new technique also suggests a range of complementary techniques that may allow future studies to pursue traces of original colour and cuticular reinforcement in amber inclusions. Ultimately, this work serves as an introduction to the underlying principles, strengths, and limitations associated with applying SR µXRF in a palaeontological context.