bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of juvenile hormone acid O‐methyltransferase and juvenile hormone synthesis in Blattella germanica
Authors: Dominguez Claudia V. , Maestro Jose L. 
Published: April 2017

AbstractJuvenile hormone (JH), a sesquiterpenoid synthetized by the insect corpora allata (CA), plays critical roles in metamorphosis and reproduction. Penultimate or last step of JH synthesis is catalyzed by juvenile hormone acid O‐methyltransferase (JHAMT). Here we report the cloning and expression analysis of the JHAMT orthologue in the cockroach, Blattella germanica (L.) (BgJHAMT). BgJHAMT is mainly expressed in CA, with only expression traces in ovary. Three different isoforms, differing in the 3′‐UTR sequence, were identified. Isoform A shows between 35 and 65 times higher expression than B and C in CA from penultimate nymphal instar and adult females. RNAi‐triggered knock down of BgJHAMT produces a dramatic reduction of JH synthesis, concomitant with a decrease of fat body vitellogenin expression and basal follicle length. BgJHAMT mRNA levels in CA of females along the gonadotrophic cycle parallel, with a slight advancement, JH synthesis profile. BgJHAMT mRNA levels were reduced in starved females and in females in which we reduced nutritional signaling by knocking down insulin receptor and target of rapamycin (TOR). Results show that conditions that modify JH synthesis in adult B. germanica females show parallel changes of BgJHAMT mRNA levels and that the JH‐specific branch of the JH synthesis pathway is regulated in the same way as the mevalonate branch. Furthermore, we demonstrate that nutrition and its signaling through the insulin receptor and TOR pathways are essential for activating BgJHAMT expression, which suggests that this enzyme can be a checkpoint for the regulation of JH production in relation to nutritional status.
Graphics for relatedness research
Authors: Galván‐Femenía Iván , Graffelman Jan , Barceló‐i‐Vidal Carles 
Published: April 2017

AbstractStudies of relatedness have been crucial in molecular ecology over the last decades. Good evidence of this is the fact that studies of population structure, evolution of social behaviours, genetic diversity and quantitative genetics all involve relatedness research. The main aim of this article was to review the most common graphical methods used in allele sharing studies for detecting and identifying family relationships. Both IBS‐ and IBD‐based allele sharing studies are considered. Furthermore, we propose two additional graphical methods from the field of compositional data analysis: the ternary diagram and scatterplots of isometric log‐ratios of IBS and IBD probabilities. We illustrate all graphical tools with genetic data from the HGDP‐CEPH diversity panel, using mainly 377 microsatellites genotyped for 25 individuals from the Maya population of this panel. We enhance all graphics with convex hulls obtained by simulation and use these to confirm the documented relationships. The proposed compositional graphics are shown to be useful in relatedness research, as they also single out the most prominent related pairs. The ternary diagram is advocated for its ability to display all three allele sharing probabilities simultaneously. The log‐ratio plots are advocated as an attempt to overcome the problems with the Euclidean distance interpretation in the classical graphics.
Spatially balanced designs that incorporate legacy sites
Authors: Foster Scott D. , Hosack Geoffrey R. , Lawrence Emma , Przeslawski Rachel , Hedge Paul , Caley M. Julian , Barrett Neville S. , Williams Alan , Li Jin , Lynch Tim , Dambacher Jeffrey M. , Sweatman Hugh P.A. , Hayes Keith R. 
Published: April 2017

Summary

A robust scientific conclusion is the result of a rigorous scientific process. In observational ecology, this process involves making inferences about a population from a sample. The sample is crucial, and is the result of implementing a survey design. A good survey design ensures that the data from the survey are capable of answering the research question. Better designs, such as spatially balanced designs, will also be as precise as possible given the constraints of the budget.

Many study areas will have previously sampled ‘legacy sites’ that already have accumulated a time series of observations. For estimating trent, it is often beneficial to include these sites within a new survey. In this paper, we propose a method to incorporate the locations of legacy sites into new spatially balanced survey designs to ensure spatial balance among all sample locations.

Simulation experiments indicate that incorporating the spatial location of legacy sites increases spatial balance and decreases uncertainty in inferences (smaller standard errors in mean estimates) when compared to designs that ignore legacy site locations. We illustrate the process of incorporating legacy sites using a proposed survey of a large marine reserve in South‐Eastern Australia, although the method is applicable to all environments.

Our approach allows for integration of legacy sites into a new spatially balanced design, increasing efficiency. Scientists, managers and funders alike will benefit from this methodology – it provides a tool to provide efficient survey designs around established ones, including in‐the‐field adjustments. In this way, it can aid integrated monitoring programmes. An R‐package that implements these methods, called MBHdesign, is available from CRAN.
Single‐node vs. multi‐node centrality in landscape graph analysis: key habitat patches and their protection for 20 bird species in NE Spain
Authors: Pereira Juliana , Saura Santiago , Jordán Ferenc 
Published: April 2017

Summary

Habitat connectivity is a major concern in biodiversity conservation. Network analysis provides efficient tools for assessing landscape connectivity and identifying priority areas for protection. Widespread approaches consist of ranking individual habitat patches by their importance for connectivity. However, depending on the spatial arrangement of patches, and on the complementarity or redundancies between different patches in the network, the group of patches that together best contribute to connectivity may differ from the top individual patches.

Here we apply individual ranking (single‐node) and group prioritization (multi‐node) methods to identify key patches in the habitat network of 20 bird species in Catalonia, Spain. We compare single‐node evaluation using the landscape index probability of connectivity (PC) and two multi‐node evaluations that focus on two different aspects of connectivity: reachability and fragmentation. We quantify how well the species’ habitats and key patches are covered by the Natura 2000 network of protected areas, as given by all three methods. We discuss some species‐specific differences between results, and general, multi‐species solutions.

The key patches for reachability were widely scattered, while patches that best prevented fragmentation were concentrated in core areas. Key patches according to single‐node PC were in intermediate position, although more similar to the fragmentation patches. The patches that minimized fragmentation were highlighted as more crucial for low‐mobility species, while reachability patches scored higher for long‐distance dispersers. For most species, the key patches were not better protected than total habitat. We identify two main areas that concentrate priority patches for all the studied species (including the endangered Neophron percnopterus) and offer suggestions for the potential improvement of the Natura 2000 network.

Our work provides a significant step towards the inclusion of multi‐node prioritization in landscape network analysis. The concept of multi‐node reachability, especially, provides an additional viewpoint to the assessment of connectivity. The multi‐patch algorithm we applied optimizes efficiency, overcoming computational limits associated with the high number of combinations that potentially arise in multi‐node analysis. We believe that a combination of multi‐node evaluations and PC has the potential to increase the realism and applicability of landscape network analysis for biodiversity conservation.
frair: an R package for fitting and comparing consumer functional responses
Authors: Pritchard Daniel W. , Paterson Rachel A. , Bovy Helene C. , Barrios‐O'Neill Daniel 
Published: April 2017

SummaryConsumer‐resource interactions (i.e. the functional response) underpin decades of ecological advancements. However, selecting, fitting and comparing functional response models using appropriate methods remains a non‐trivial endeavour.The R packagefrairprovides tools for selecting and differentiating various forms of consumer functional response models, a consistent interface for fitting and visualising response curves, and a selection of statistically robust methods for comparing fitted parameters.Using real data from crustacean predator‐prey systems, we demonstrate the utility offrair, highlighting best practice and common analytical mistakes.
From animal tracks to fine‐scale movement modes: a straightforward approach for identifying multiple spatial movement patterns
Authors: Morelle Kevin , Bunnefeld Nils , Lejeune Philippe , Oswald Stephen A. 
Published: April 2017

SummaryThanks to developments in animal tracking technology, detailed data on the movement tracks of individual animals are now attainable for many species. However, straightforward methods to decompose individual tracks into high‐resolution, spatial modes are lacking but are essential to understand what an animal is doing.We developed an analytical approach that combines separately validated methods into a straightforward tool for converting animalGPStracks into short‐range movement modes. Our three‐step analytical process comprises: (i) decomposing data into separate movement segments using behavioural change point analysis; (ii) defining candidate movement modes and translating them into nonlinear or linear equations between net squared displacement (NSD) and time and (iii) fitting each candidate equation toNSDsegments and determining the best‐fitting modes using Concordance Criteria, Akaike's Information Criteria and other fine‐scale segment characteristics. We illustrate our approach for three sub‐adults, male wild boarSus scrofatracked at 15‐min intervals over 4 months usingGPScollars. We defined five candidate movement modes based on previously published studies of short‐term movements: encamped, ranging, round trips (complete and partial) and wandering.Our approach successfully classified over 80% of the tracks into these movement modes lasting between 5 and 54 h and covering between 300 m to 20 km. Repeated analyses ofGPSdata resampled at different rates indicated that one positional fix every 3–4 h was sufficient for >70% classification success. Classified modes were consistent with published observations of wild boar movement, further validating our method.The proposed approach advances the status quo by permitting classification into multiple movement modes (where these are adequately discernable from spatial fixes) facilitating analyses at high temporal and spatial resolutions, and is straightforward, largely objective, and without restrictive assumptions, necessary parameterizations or visual interpretation. Thus, it should capture the complexity and variability of tracked animal movement mode for a variety of taxa across a wide range of spatial and temporal scales.
HistMapR: Rapid digitization of historical land‐use maps in R
Authors: Auffret Alistair G. , Kimberley Adam , Plue Jan , Skånes Helle , Jakobsson Simon , Waldén Emelie , Wennbom Marika , Wood Heather , Bullock James M. , Cousins Sara A.O. , Gartz Mira , Hooftman Danny A.P. , Tränk Louise 
Published: April 2017

Summary

Habitat destruction and degradation represent serious threats to biodiversity, and quantification of land‐use change over time is important for understanding the consequences of these changes to organisms and ecosystem service provision.

Comparing land use between maps from different time periods allows estimation of the magnitude of habitat change in an area. However, digitizing historical maps manually is time‐consuming and analyses of change are usually carried out at small spatial extents or at low resolutions.

HistMapR contains a number of functions that can be used to semi‐automatically digitize historical land use according to a map's colours, as defined by the RGB bands of the raster image. We test the method on different historical land‐use map series and compare results to manual digitizations.

Digitization is fast, and agreement with manually digitized maps of around 80–90% meets common targets for image classification. We hope that the ability to quickly classify large areas of historical land use will promote the inclusion of land‐use change into analyses of biodiversity, species distributions and ecosystem services.
Emergency Department Vital Signs and Outcomes After Discharge
Authors: Gabayan Gelareh Z. , Gould Michael K. , Weiss Robert E. , Derose Stephen F. , Chiu Vicki Y. , Sarkisian Catherine A. 
Published: April 2017

AbstractObjectiveVital signs are critical markers of illness severity in the emergency department (ED). Providers need to understand the abnormal vital signs in older adults that are problematic. We hypothesized that in patients age > 65 years discharged from the ED, there are abnormal vital signs that are associated with an admission to an inpatient bed within 7 days of discharge.MethodsWe conducted a retrospective cohort study using data from a regional integrated health system of members age > 65 years during the years 2009 to 2010. We used univariate contingency tables to assess the relationship between hospital admission within 7 days of discharge and vital sign (including systolic blood pressure [sBP], heart rate [HR], body temperature, and pulse oximetry [SpO2] values measured closest to discharge) using standard thresholds for abnormal and thresholds derived from the study data.ResultsOf 104,025 ED discharges, 4,638 (4.5%) were followed by inpatient admission within 7 days. Vital signs had a greater odds of admission beyond a single cutoff. The vital signs with at least twice the odds of admission were sBP < 97 mm Hg (odds ratio [OR] = 2.02, 95% CI = 1.57–2.60), HR > 101 beats/min (OR = 2.00 95% CI = 1.75–2.29), body temperature > 37.3°C (OR = 2.14, 95% CI = 1.90–2.41), and pulse oximetry < 92 SpO2 (OR = 2.04, 95% CI = 1.55–2.68). Patients with two vital sign abnormalities per the analysis had the highest odds of admission. A majority of patients discharged with abnormal vital signs per the analysis were not admitted within 7 days of ED discharge.ConclusionWhile we found a majority of patients discharged with abnormal vital signs as defined by the analysis, not to be admitted after discharge, we identified vital signs associated with at least twice the odds of admission.
Community demographics, socio‐economic and health status among older Australian residents of Japanese origin living in New South Wales, Australia
Authors: Watanabe Yuriko , Honda Kazuma 
Published: April 2017

ObjectiveThis study aimed to describe demographic and socio‐economic characteristics and to assess baseline health status and care needs among Japanese residents aged 60 years and over living in New South Wales, Australia.MethodsA postal questionnaire was used to survey older community‐dwelling Japanese residents recruited from a number of different sources.ResultsEighty‐two residents responded to the questionnaire (mean age: 70.5 years, range 60–85), and 56 (68.3%) were female. The respondents appeared to be socio‐economically comfortable. While 63.4% of respondents noticed reduced strength and balance, and 45% had at least one chronic medical condition, the majority did not require help with personal care or domestic chores. However, there were respondents who were considered at risk of subsequent development of major mobility limitations.ConclusionOverall, the respondents in this study demonstrated good function. There may be a role for interventional programs aimed at maintaining functional independence.
Genome‐wide expression profiling and bioinformatics analysis of deregulated genes in human gastric cancer tissue after gastroscopy
Authors: Mao Yudi , Zhao Qihong , Yin Shi , Ding Xiping , Wang Hua 
Published: April 2017

AbstractAimThe aim of this study was to analyze the gene expression profile and biological processes enriched in gastric cancer.MethodsWe collected five human advanced gastric cancer tissues by gastroscopy and five peritumor normal tissues as controls and examined the gene expression changes by microarray. KEGG Orthology Based Annotation System annotation was used to identify pathways and biological processes regulated by the deregulated genes. Protein–protein interaction network analysis identified protein complex and functional modules. We also selected 14 genes for further verification by real‐time quantitative Polymerase Chain Reaction (PCR).ResultsHuman gene expression profile analysis showed that 2028 deregulated genes were detected in gastric cancer compared with the control group (at least a 2.0‐fold change and P < 0.05), among which there were 689 upregulated and 1339 downregulated genes. Interestingly, we identified some important genes, such as CXCL17, OTX1 and CCDC125, which have not previously been reported in gastric cancer. Real‐time quantitative PCR results verified that CXCL8, OTX1, CEBPB, FOSL1, FOXS1, ARFRP1 and IRF9 were upregulated in gastric cancer and CCDC125, PPP1R36, SOX2, JUN and MIA2 were downregulated. Moreover, bioinformatics analysis demonstrated that the biological processes of inflammatory response, angiogenesis, cell migration and pathways of chemokine signaling pathway, TNF signaling pathway were enriched. We also selected the top 30 significant Gene Ontology terms and select pathways for a brief summary.ConclusionWe performed a global analysis of the mRNA landscape in gastric cancer. Our results may stimulate a deeper understanding of the disease, and lead to the development of potential therapies and the identification of novel biomarkers.
Intrapartum and neonatal outcomes in singleton pregnancies following conception by assisted reproduction techniques
Authors: Rozdarz Kellie M. , Flatley Christopher J. , Kumar Sailesh 
Published: April 2017

BackgroundTo characterise maternal demographics and ascertain whether clinically important differences exist in the intrapartum and neonatal outcomes associated with assisted reproductive technology (ART).Materials and methodsA retrospective study was undertaken between January 2007 and December 2013 of all singleton pregnancies conceived via ART at a major tertiary unit in Brisbane, Australia. Intrapartum outcomes were mode of delivery and indication for emergency caesarean. Neonatal outcomes investigated were gestation at delivery, birth weight, Apgar scores, acidosis at birth, respiratory distress, need for resuscitation, admission to neonatal intensive care and stillbirth.ResultsThere were 4733 (7.4%) ART and 59 277 (92.6%) spontaneous conception pregnancies. Women who conceived using ART were less likely to have a spontaneous vaginal delivery (odds ratio (OR) 0.60, 95% CI 0.57–0.64) and were more likely to require operative or assisted birth: elective caesarean (adjusted OR (aOR) 1.31, 95% CI 1.22–1.40), emergency caesarean (aOR 1.19, 95% CI 1.09–1.28), or instrumental delivery (aOR 1.45, 95% CI 1.32–1.58). Neonates who were conceived using ART were less likely to be born at term (aOR 0.64, 95% CI 0.58–0.71) and have lower birth weights. No differences were observed in rates of respiratory distress, admission to the neonatal intensive care unit, or stillbirth between the ART and spontaneous conception cohorts. The odds of neonatal acidosis (OR 0.71, 95% CI0.63–0.81) were lower in the ART cohort.ConclusionAlthough higher rates of operative deliveries were seen for women who conceive using ART, neonatal outcomes were generally no different between the two cohorts.
Dynamics of Policymaking: Stepping Back to Leap Forward, Stepping Forward to Keep Back
Authors: Buisseret Peter , Bernhardt Dan 
Published: April 2017

AbstractWe study dynamic policymaking when today's policy agreement becomes tomorrow's status quo, agents account for the consequences of today's policies for future policy outcomes, and there is uncertainty about who will hold future political power to propose and veto future policy changes. Today's agenda setter holds back from fully exploiting present opportunities to move policy toward her ideal point whenever future proposer and veto players are likely to be alignedeitherin favor of reform or against it. Otherwise, agenda setters advance their short‐run interests. Optimal proposals can vary discontinuously and nonmonotonically with political fundamentals.
Cervical collagen is reduced in non‐pregnant women with a history of cervical insufficiency and a short cervix
Authors: Sundtoft Iben , Langhoff‐Roos Jens , Sandager Puk , Sommer Steffen , Uldbjerg Niels 
Published: April 2017

AbstractIntroductionPreterm cervical shortening and cervical insufficiency may be caused by a constitutional weakness of the cervix. The aim of this study was to assess the cervical collagen concentration in non‐pregnant women with a history of cervical insufficiency or of a short cervix in the second trimester of pregnancy.Material and methodsIn this case‐control study we included non‐pregnant women one year or more after pregnancy: 55 controls with a history of normal delivery; 27 women with a history of cervical insufficiency; and 10 women with a history of a short cervix (<5th percentile) and 10 women with a history of a long cervix (>95th percentile) at gestational weeks 18–20. We obtained biopsies (3 × 3–4 mm) from the ectocervix and determined the collagen concentration by measuring the hydroxyproline concentration.ResultsWomen with cervical insufficiency had lower collagen concentrations (63.5 ± 5.1%; mean ± SD) compared with controls (68.2 ± 5.4%; p = 0.0004); area under the ROC curve 0.73 (95% CI 0.62–0.84). A cut‐off value at 67.6% collagen resulted in a positive likelihood ratio of 3.2, a sensitivity of 60%, and a specificity of 81%. Also, women with a short cervix in the second trimester had lower collagen concentrations in a non‐pregnant state (62.1% ± 4.9%) compared with women with a long cervix (67.8% ± 5.0%; p = 0.02).Conclusions. Both cervical insufficiency and a short cervix in the second trimester of pregnancy are associated with low cervical collagen concentrations in a non‐pregnant state more than one year after pregnancy.