bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network size, structure and mutualism dependence affect the propensity for plant–pollinator extinction cascades
Authors: Vanbergen Adam J. , Woodcock Ben A. , Heard Matthew S. , Chapman Daniel S. 
Published: December 2016

Summary

Pollinator network structure arising from the extent and strength of interspecific mutualistic interactions can promote species persistence and community robustness. However, environmental change may re‐organise network structure limiting capacity to absorb or resist shocks and increasing species extinctions.

We investigated if habitat disturbance and the level of mutualism dependence between species affected the robustness of insect–flower visitation networks Following a recently developed Stochastic Co‐extinction Model (SCM), we ran simulations to produce the number of extinction episodes (cascade degree), which we correlated with network structure in undisturbed and disturbed habitat. We also explicitly modelled whether a species’ intrinsic dependence on mutualism affected the propensity for extinction cascades in the network.

Habitat disturbance generated a gradient in network structure with those from disturbed sites being less connected, but more speciose and so larger. Controlling for network size (z‐score standardisation against the null model) revealed that disturbed networks had disproportionately low linkage density, high specialisation, fewer insect visitors per plant species (vulnerability) and lower nestedness (NODF).

This network structure gradient driven by disturbance increased and decreased different aspects of robustness to simulated plant extinction. Disturbance decreased the risk that an initial insect extinction would follow a plant species loss. Although, this effect disappeared when network size and connectance were standardised, suggesting the lower connectance of disturbed networks increased robustness to an initial secondary extinction.

However, if a secondary extinction occurred then networks from disturbed habitat were more prone to large co‐extinction cascades, likely resulting from a greater chance of extinction in these larger, speciose networks. Conversely, when species mutualism dependency was explicit in the SCM simulations the disturbed networks were disproportionately more robust to very large co‐extinction cascades, potentially caused by non‐random patterns of interaction between species differing in dependence on mutualism.

Our results showed disturbance altered the size and the distribution of interspecific interactions in the networks to affect their robustness to co‐extinction cascades. Controlling for effects due to network size and the interspecific variation in demographic dependence on mutualism can improve insight into properties conferring the structural robustness of networks to environmental changes.

A lay summary is available for this article.
Coping with inevitable accidents in metabolism
Authors: Danchin Antoine 
Published: December 2016

SummaryGenomic studies focus on key metabolites and pathways that, despite their obvious anthropocentric design, keep being ‘predicted’, while this is only finding again what is already known. As increasingly more genomes are sequenced, this lightpost effect may account at least in part for our failure to understand the function of a continuously growing number of genes. Core metabolism often goes astray, accidentally producing a variety of unexpected compounds. Catabolism of these forgotten metabolites makes an essential part of the functions coded in metagenomes. Here, I explore the fate of a limited number of those: compounds resulting from radical reactions and molecules derived from some reactive intermediates produced during normal metabolism. I try both to update investigators with the most recent literature and to uncover old articles that may open up new research avenues in the genome exploration of metabolism. This should allow us to foresee further developments in experimental genomics and genome annotation.
The Origin and Tectonic Setting of Precambrian Greywacke of Ribandar‐Chimbel, Goa, India: Petrological and Geochemical Evidence
Authors: FERNANDES Glancia Q , IYER Sridhar D. , KOTHA Mahender 
Published: December 2016

AbstractThe Precambrian greywacke of Ribandar‐Chimbel belonging to the Sanvordem Formation of the Goa Group, India, has been studied for petrography and analyzed for major trace elements. The greywacke is characterized by angular to sub‐round grains of quartz, feldspar, biotite, chlorite and clay minerals. The abundance of clay in the matrix seems to have influenced the Al2O3 content and the K2O/Al2O3 ratio. The variation diagrams indicate a decreasing trend of TiO2, Al2O3, Fe2O3 and MgO; whereas Na2O and CaO exhibit a scatter which could be a result of the variable presence of feldspar within the sediments. The immobile elements, vanadium (25 to 144 ppm), nickel (up to 107 ppm) and chromium (up to 184 ppm), reflect abundance of clay minerals. The greywacke shows strongly fractionated REE patterns with LaN/YbN = 8 to 26 and with higher total REE abundances (up to 245 ppm). The low REE enrichment and depletion in heavier REE with prominent negative Eu anomaly (Eu/Eu*= 0.54 to 0.79) suggest a derivation of the greywacke from an old upper continental crust composed chiefly of felsic components. Petrological evidence and geochemical data suggest that the deposition of the greywacke largely took place in a deep to shallow basin that progressively changed from that of a continental island arc to an active continental setting.
Reservoir Characteristics and Preservation Conditions of Longmaxi Shale in the Upper Yangtze Block, South China
Authors: RAN Bo , LIU Shugen , JANSA Luba , SUN Wei , YANG Di , WANG Shiyu , YE Yuehao , XIAO Christopher , ZHANHG Jian , ZHAI Cangbo , LUO Chao , ZHANG Changjun 
Published: December 2016

AbstractThe Upper Ordovician‐Lower Silurian Longmaxi Shale in the Upper Yangtze block represents one of the most important shale gas plays in China. The shale composition, porosity, organic thermal maturity, and methane sorption were investigated at the Qilongcun section in the Dingshan area, southeastern Sichuan Basin. The results show that the Upper Ordovician‐Lower Silurian Longmaxi Shale contains: (1) sapropelic I organic matter; (2) a 40‐m thick bedded sequence where total organic carbon (TOC) content is > 2%; (3) a 30m thick layer at the base of the Longmaxi Shale with a brittle mineral content higher than 50%; and (4) a mean methane adsorption capacity of 1.80 cm3/g (7 MPa pressure). A positive correlation between TOC and sorbed gas indicates that organic matter content exerts an important control on methane storage capacity. Based on the analysis of the shale reservoir characteristics, the lower member of the Longmaxi Shale can thus be considered a favorable stratum for shale gas exploration and exploitation. It has similar reservoir characteristics with the Longmaxi Shale in the Jiaoshiba area tested with a high‐yield industrial gas flow. However, based on tectonic analysis, differences in the level of industrial gas flow between the low‐yield study area and the high‐yield Jiaoshiba area may result from different tectonic preservation conditions. Evidence from these studies indicates the shale gas potential of the Longmaxi Shale is constrained by the reservoir and preservation conditions.
The impact of lions on the demography and ecology of endangered African wild dogs
Authors: Groom R. J. , Lannas K. , Jackson C. R. 
Published: December 2016

AbstractIt has long been recognized that superior carnivores can impact on the demography and ecology of smaller members of the guild, although exact mechanisms remain unclear. Here we use original data from a unique natural experiment to study some of the mechanisms by which African lions Panthera leo impact on African wild dogs Lycaon pictus. Using a study site where wild dogs outnumbered lions for several years prior to lion population recovery, we aimed to investigate whether or not, and by which means, wild dog populations are regulated and influenced by lions. We used 38 pack‐years of demographic and behavioural data across two 4‐year periods where lion density differed 20‐fold (pre‐lion era: 1996–1999 and lion era: 2010–2013) to assess how lions may affect wild dog pack size and age structure, litter size and pup survival (n = 329 pups), as well as den site selection (n = 46 dens). Pack size was significantly greater during the pre‐lion era. The pup to adult ratio was lower during the lion era and the change in pack composition was directly attributable to significantly greater lion‐induced pup mortality. We also demonstrate a behavioural shift, with locations selected for the vulnerable denning period being in more rugged terrain and in areas with lower prey densities during the lion era, as compared with the pre‐lion era. Lower adult recruitment into a population of an obligate cooperative breeder like the African wild dog can have complex consequences, including on feeding and defence of young, and mate finding.
The heterogeneous farm‐level impact of the 2005 CAP‐first pillar reform: A multivalued treatment effect estimation
Authors: Esposti Roberto 
Published: December 2016

AbstractThis article aims to evaluate the impact of the 2005 reform of the Common Agricultural Policy (CAP) on farm production choices as a treatment effect (TE). This impact is measured through alternative metrics of the short‐term changes of the output vector. The heterogeneity of the response to the reform is assessed by estimating both average and quantile TE. As this heterogeneous response may depend on the different farm‐level CAP support, a multivalued treatment approach is adopted and applied to treated units (i.e., supported farms). This approach is applied to a balanced panel of Italian FADN farms observed over years 2003–2007. Results show that the 2005 reform of the first pillar of the CAP actually had an impact in (re)orienting short‐term farm production choices but this response is largely heterogeneous and concentrated in the lower levels of support.
Disease‐Concordant Twins Empower Genetic Association Studies
Authors: Tan Qihua , Li Weilong , Vandin Fabio 
Published: December 2016

SummaryGenome‐wide association studies with moderate sample sizes are underpowered, especially when testing SNP alleles with low allele counts, a situation that may lead to high frequency of false‐positive results and lack of replication in independent studies. Related individuals, such as twin pairs concordant for a disease, should confer increased power in genetic association analysis because of their genetic relatedness. We conducted a computer simulation study to explore the power advantage of the disease‐concordant twin design, which uses singletons from disease‐concordant twin pairs as cases and ordinary healthy samples as controls. We examined the power gain of the twin‐based design for various scenarios (i.e., cases from monozygotic and dizygotic twin pairs concordant for a disease) and compared the power with the ordinary case‐control design with cases collected from the unrelated patient population. Simulation was done by assigning various allele frequencies and allelic relative risks for different mode of genetic inheritance. In general, for achieving a power estimate of 80%, the sample sizes needed for dizygotic and monozygotic twin cases were one half and one fourth of the sample size of an ordinary case‐control design, with variations depending on genetic mode. Importantly, the enriched power for dizygotic twins also applies to disease‐concordant sibling pairs, which largely extends the application of the concordant twin design. Overall, our simulation revealed a high value of disease‐concordant twins in genetic association studies and encourages the use of genetically related individuals for highly efficiently identifying both common and rare genetic variants underlying human complex diseases without increasing laboratory cost.
Opisthorchis felineus negatively associates with skin test reactivity in Russia—EuroPrevall‐International Cooperation study
Authors: Fedorova O. S. , Janse J. J. , Ogorodova L. M. , Fedotova M. M. , Achterberg R. A. , Verweij J. J. , Fernández‐Rivas M. , Versteeg S. A. , Potts J. , Minelli C. , van Ree R. , Burney P. , Yazdanbakhsh M. 
Published: December 2016

AbstractBackgroundMost studies on the relationship between helminth infections and atopic disorders have been conducted in (sub)tropical developing countries where exposure to multiple parasites and lifestyle can confound the relationship. We aimed to study the relationship between infection with the fish‐borne helminth Opishorchis felineus and specific IgE, skin prick testing, and atopic symptoms in Western Siberia, with lifestyle and hygiene standards of a developed country.MethodsSchoolchildren aged 7–11 years were sampled from one urban and two rural regions. Skin prick tests (SPT) and specific IgE (sIgE) against food and aeroallergens were measured, and data on allergic symptoms and on demographic and socioeconomic factors were collected by questionnaire. Diagnosis of opisthorchiasis was based on PCR performed on stool samples.ResultsOf the 732 children included, 34.9% had opisthorchiasis. The sensitization to any allergen when estimated by positive SPT was 12.8%, while much higher, 24.0%, when measured by sIgE. Atopic symptoms in the past year (flexural eczema and/or rhinoconjunctivitis) were reported in 12.4% of the children. SPT was positively related to flexural eczema and rhinoconjunctivitis, but not to wheezing. Opisthorchiasis showed association with lower SPT response, as well as borderline association with low IgE reactivity to any allergen. However, the effect of opisthorchiasis on SPT response was not mediated by IgE, suggesting that opisthorchiasis influences SPT response through another mechanism. Opisthorchiasis also showed borderline association with lower atopic symptoms.ConclusionsThere is a negative association between a chronic helminth infection and skin prick test reactivity even in a developed country.
Prediction of progression to severe disease in women with late preterm hypertensive disorders of pregnancy
Authors: Zwertbroek Eva F. , Broekhuijsen Kim , Langenveld Josje , van Baaren Gert‐Jan , van den Berg Paul P. , Bremer Henk A. , Ganzevoort Wessel , van Loon Aren J. , Mol Ben W.J. , van Pampus Maria G. , Perquin Denise A.M. , Rijnders Robbert J.P. , Scheepers Hubertina C.J. , Sikkema Marko J. , Woiski Mallory D. , Groen Henk , Franssen Maureen T.M. ,   the HYPITAT‐II Study Group
Published: December 2016

AbstractIntroductionIf hypertensive disorders of pregnancy are diagnosed before term, the benefits of immediate delivery need to be weighed against the neonatal consequences of preterm delivery. If we are able to predict which women are at high risk of progression to severe disease, they could be targeted for delivery and maternal complications might be reduced. In addition, this may prevent unnecessary preterm births in women at low risk.Material and methodsWe developed a prediction model using data from the HYPITAT‐II trail, which evaluated immediate delivery vs. expectant monitoring in women with non‐severe hypertensive disorders of pregnancy between 34 and 37 weeks of gestation. Univariate and multivariate logistic regression analysis were used to identify relevant variables from clinical and laboratory parameters. The performance of the resulting prediction model was assessed by receiver operating characteristic analysis, calibration and bootstrapping, using the average predicted probabilities.ResultsWe included 519 women, 115 (22.2%) of whom developed severe hypertensive disorders of pregnancy. The prediction model included: maternal age (odds ratio 0.92 per year), gestational age (odds ratio 0.87 per week), systolic blood pressure (odds ratio 1.05 per mmHg), the presence of chronic hypertension (odds ratio 2.4), platelet count (odds ratio 0.996), creatinine (odds ratio 1.02) and lactate dehydrogenase (odds ratio 1.003). The model showed good fit (p = 0.64), fair discrimination (area under the curve 0.76, 95% confidence interval 0.73–0.81, p < 0.001) and could stratify women in three risk groups of average, intermediate and high risk (predicted probabilities <0.22, <0.44 and >0.45, respectively).ConclusionIn women with non‐severe hypertension in pregnancy near term, progression to severe disease can be predicted. This model requires external validation before it can be applied in practice.
Multicompartment compliance aids in the community: the prevalence of potentially inappropriate medications
Authors: Counter David , Stewart Derek , MacLeod Joan , McLay James S. 
Published: December 2016

AimsTo assess the prevalence of potentially inappropriate medications (PIMs) use in a population of community‐based multicompartment compliance aid (MCA) users in north‐east Scotland.MethodsData for MCAs dispensed by 48 of the 50 community pharmacies in Aberdeen City between 1st June to 31st October 2014, together with concurrently prescribed medications, patient demographics and Carstairs index of social deprivation were recorded. Drug‐specific quality indicators for PIMs from the Swedish National Board of Health and Welfare were applied and bivariate logistic regression analysis used to assess for associations with demographic variables.ResultsThe median age was 82 years (range 12–105 years, 59% female). A total of 1977 PIMs were identified affecting 57.8% of patients. A quarter of patients were prescribed ≥10 medications and 43% had a prescription containing at least one clinically significant drug–drug interaction (DDI). Ten drug groups accounted for 76% of all DDIs. A significant increase in the risk for at least one PIM was associated with female sex (for all indicators of PIM use), age <80 years (three or more psychotropic medicines [OR 5.88, 2.96–11.70, P < 0.001]) and lower socioeconomic status (prescription of ≥10 medications [OR: 1.43, 95% CI: 1.16–1.78], prescription of a long‐acting benzodiazepine [OR: 1.84, CI: 1.14–2.98]).ConclusionsMCA use is associated with a significant incidence of PIMs particularly affecting those younger than 80 years and those living in deprived areas. Our findings indicate the need for a more aggressive multidisciplinary approach to the review of the medications prescribed to MCA users.
Mass Spectrometry‐Based Tools to Characterize DNA–Protein Cross‐Linking by Bis‐Electrophiles
Authors: Groehler Arnold , Degner Amanda , Tretyakova Natalia Y. 
Published: December 2016

AbstractDNA–protein cross‐links (DPCs) are unusually bulky DNA adducts that form in cells as a result of exposure to endogenous and exogenous agents including reactive oxygen species, ultraviolet light, ionizing radiation, environmental agents (e.g. transition metals, formaldehyde, 1,2‐dibromoethane, 1,3‐butadiene) and common chemotherapeutic agents. Covalent DPCs are cytotoxic and mutagenic due to their ability to interfere with faithful DNA replication and to prevent accurate gene expression. Key to our understanding of the biological significance of DPC formation is identifying the proteins most susceptible to forming these unusually bulky and complex lesions and quantifying the extent of DNA–protein cross‐linking in cells and tissues. Recent advances in bottom‐up mass spectrometry‐based proteomics have allowed for an unbiased assessment of the whole protein DPC adductome after in vitro and in vivo exposures to cross‐linking agents. This MiniReview summarizes current and emerging methods for DPC isolation and analysis by mass spectrometry‐based proteomics. We also highlight several examples of successful applications of these novel methodologies to studies of DPC lesions induced by bis‐electrophiles such as formaldehyde, 1,2,3,4‐diepoxybutane, nitrogen mustards and cisplatin.
The human genome as public: Justifications and implications
Authors: Bayefsky Michelle J. 
Published: December 2016

AbstractSince the human genome was decoded, great emphasis has been placed on the unique, personal nature of the genome, along with the benefits that personalized medicine can bring to individuals and the importance of safeguarding genetic privacy. As a result, an equally important aspect of the human genome – its common nature – has been underappreciated and underrepresented in the ethics literature and policy dialogue surrounding genetics and genomics. This article will argue that, just as the personal nature of the genome has been used to reinforce individual rights and justify important privacy protections, so too the common nature of the genome can be employed to support protections of the genome at a population level and policies designed to promote the public's wellbeing.In order for public health officials to have the authority to develop genetics policies for the sake of the public good, the genome must have not only a common, but also a public, dimension. This article contends that DNA carries a public dimension through the use of two conceptual frameworks: the common heritage (CH) framework and the common resource (CR) framework. Both frameworks establish a public interest in the human genome, but the CH framework can be used to justify policies aimed at preserving and protecting the genome, while the CR framework can be employed to justify policies for utilizing the genome for the public benefit. A variety of possible policy implications are discussed, with special attention paid to the use of large‐scale genomics databases for public health research.
Bithalamic gliomas may be molecularly distinct from their unilateral high‐grade counterparts
Authors: Broniscer Alberto , Hwang Scott N. , Chamdine Omar , Lin Tong , Pounds Stanley , Onar‐Thomas Arzu , Chi Lei , Shurtleff Sheila , Allen Sariah , Gajjar Amar , Northcott Paul , Orr Brent A. 
Published: December 2016

AbstractBithalamic gliomas are rare cancers diagnosed based on poorly defined radiologic criteria. Infiltrative astrocytomas account for most cases. While some previous studies reported dismal outcomes for patients with bithalamic gliomas irrespective of therapy and histologic grade, others described better prognoses even without anticancer therapy. Little is known about their molecular characteristics. We reviewed clinical, radiologic, and histologic features of patients with bithalamic gliomas treated at our institution over 15 years. Targeted sequencing of mutational hotspots in H3F3A, HIST1H3B, IDH1/2, and BRAF, and genome‐wide analysis of DNA methylation and copy number abnormalities was performed in available tumors. Eleven patients with bithalamic gliomas were identified. Their median age at diagnosis was 4.8 years (range: 1–15.7). Additional involvement of the brainstem, basal ganglia, and cerebral lobes occurred in 11, 9, and 3 cases, respectively. All patients presented with hydrocephalus. Two‐thirds of the patients had a histologic diagnosis of anaplastic astrocytoma. Despite aggressive therapy, our youngest patient, the only one diagnosed before 1 year of age, is the sole long‐term survivor. DNA methylation could be performed in seven tumors, all of which clustered with the RTK I ‘PDGFRA’ subgroup by unsupervised hierarchical analysis of methylation array against a previously published cohort of 59 pediatric high‐grade gliomas. Sequencing of hotspots mutations could be done in 10 tumors, none of which harbored H3F3A p.K27 and/or the respective DNA methylation signature, and any other hotspot mutations. Amplification of MDM4 (n = 2), PDGFRA (n = 2), and ID2 combined with MYCN (n = 1) were observed in 7 tumors available for analysis. In comparison with the previously published experience with unilateral high‐grade thalamic astrocytomas where H3F3A p.K27 was present in two‐thirds of cases, the absence of this molecular subgroup in bithalamic gliomas was striking. This finding suggests that unilateral and bithalamic high‐grade gliomas may represent two distinct molecular entities.