bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-reported patient history to assess hepatitis B virus serological status during a large screening campaign
Authors: Boyd A. , Gozlan J. , Carrat F. , Rougier H. , Girard P.-M. , Lacombe K. , Bottero J. 
Published: September 2018

AbstractWhen assessing hepatitis B virus (HBV) status in clinical settings, it is unclear whether self-reports on vaccination history and previous HBV-test results have any diagnostic capacity. Of 3997 participants in a multi-centre HBV-screening study in Paris, France, 1090 were asked questions on their last HBV-test result and vaccination history. Discordance between self-reported history compared with infection status (determined by serology) was calculated for participants claiming ‘negative’, ‘effective vaccine’, ‘past infection’, or ‘chronic infection’ HBV-status. Serological testing revealed that 320 (29.4%) were non-immunised, 576 (52.8%) were vaccinated, 173 (15.9%) had resolved the infection and 21 (1.9%) were hepatitis B surface antigen positive. In total 208/426 (48.8%) participants with a self-reported history of ‘negative’ infection had a discordant serological result, in whom 128 (61.5%) were vaccinated and 74 (35.6%) had resolved infections. A total of 153/599 (25.5%) participants self-reporting ‘effective vaccine’ had a discordant serological result, in whom 100 (65.4%) were non-immunised and 50 (32.7%) were resolved infections. Discordance for declaring ‘past’ or ‘chronic infection’ occurred in 9/55 (16.4%) and 3/10 (30.0%) individuals, respectively. In conclusion, self-reported HBV-status based on participant history is partially inadequate for determining serological HBV-status, especially between negative/vaccinated individuals. More adapted patient education about HBV-status might be helpful for certain key populations.
Analyses of the internal transcribed rDNA spacers (ITS1 and ITS2) of Indian weevils of Odoiporus longicollis (Olivier) reveal gene flow between locations
Authors: Kumar Lalitha Sunil , Shankar Pallavi , Kulkarni Vishvas M. 
Published: September 2018

AbstractAn important step towards developing a successful integrated pest management (IPM) programme for the control of banana pseudostem weevil,Odoiporus longicollis(Olivier), a serious pest of banana in India, is the study of the population structure of the pest. In the present study, the genetic variation among 30 individual weevils ofO.longicolliscollected from six different locations was assessed by analysing the primary nucleotide sequences of the rDNA ITS1 and ITS2 regions. AMOVA, Mantel test, and the maximum likelihood trees of the haplotypes failed to reveal any phylogeographic structuring, which was confirmed by haplotype analysis and genetic differentiation estimates. The results indicate that the locations are not differentiated, i.e. there is gene flow between the locations. The star-shaped networks revealed a signature of demographic expansion that was confirmed by the different demographic tests. These results provide important information, which is essential for the development of suitable strategies for the control of this banana pest, as well as management of its resistance to insecticides.
Processes Controlling the Composition and Abundance of Arctic Aerosol
Authors: Willis Megan D. , Leaitch W. Richard , Abbatt Jonathan P.D. 
Published: September 2018

AbstractThe Arctic region is a harbinger of global change and is warming at a rate higher than the global average. While Arctic warming is driven by increases in anthropogenic greenhouse gases' in combination with local feedback mechanisms, short‐lived climate forcing agents, such as tropospheric aerosol, are also important drivers of Arctic climate. Arctic aerosol‐climate impacts vary seasonally as a result of the interplay between aerosol and different cloud types, available solar radiation, sea ice, surface albedo, Arctic and lower latitude removal processes, and atmospheric transport patterns. Photochemistry and efficient wet aerosol removal have low impact in winter but become important in spring to summer, dramatically altering aerosol chemical composition, and driving the size distribution from a pronounced accumulation mode toward a dominance of smaller particles. Retreating sea ice, increasing solar insolation and warmer temperatures in summer result in enhanced emissions from Arctic marine and terrestrial ecosystems, and anthropogenic sources, with impacts on the composition of gas and particle phases. Fractional cloud cover reaches a maximum in Arctic summer, in parallel with decreasing sea ice extent and surface albedo. This seasonal variation corresponds to significant changes in the net cloud radiative effect; changes that are affected by aerosol. This review summarizes our current knowledge of processes that control Arctic aerosol properties. We highlight both natural and anthropogenic processes that will be impacted by current and future sea ice loss. Efforts are needed to better constrain aerosol removal rates, characterize aerosol precursors, and constrain the seasonality and magnitude of aerosol‐cloud‐climate impacts.
Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates
Authors: Hara Yuichiro , Yamaguchi Kazuaki , Onimaru Koh , Kadota Mitsutaka , Koyanagi Mitsumasa , Keeley Sean D. , Tatsumi Kaori , Tanaka Kaori , Motone Fumio , Kageyama Yuka , Nozu Ryo , Adachi Noritaka , Nishimura Osamu , Nakagawa Reiko , Tanegashima Chiharu , Kiyatake Itsuki , Matsumoto Rui , Murakumo Kiyomi , Nishida Kiyonori , Terakita Akihisa , Kuratani Shigeru , Sato Keiichi , Hyodo Susumu , Kuraku Shigehiro 
Published: September 2018

AbstractModern cartilaginous fishes are divided into elasmobranchs (sharks, rays and skates) and chimaeras, and the lack of established whole-genome sequences for the former has prevented our understanding of early vertebrate evolution and the unique phenotypes of elasmobranchs. Here we present de novo whole-genome assemblies of brownbanded bamboo shark and cloudy catshark and an improved assembly of the whale shark genome. These relatively large genomes (3.8–6.7 Gbp) contain sparse distributions of coding genes and regulatory elements and exhibit reduced molecular evolutionary rates. Our thorough genome annotation revealed Hox C genes previously hypothesized to have been lost, as well as distinct gene repertories of opsins and olfactory receptors that would be associated with adaptation to unique underwater niches. We also show the early establishment of the genetic machinery governing mammalian homoeostasis and reproduction at the jawed vertebrate ancestor. This study, supported by genomic, transcriptomic and epigenomic resources, provides a foundation for the comprehensive, molecular exploration of phenotypes unique to sharks and insights into the evolutionary origins of vertebrates.
Genetic inhibition of an ATP synthase subunit extends lifespan in C. elegans
Authors: Xu Chen , Hwang Wooseon , Jeong Dae-Eun , Ryu Youngjae , Ha Chang Man , Lee Seung-Jae V. , Liu Lulu , He Zhi Ming 
Published: September 2018

AbstractMild inhibition of mitochondrial respiration leads to longevity. Disruption of mitochondrial respiratory components extends lifespan in Caenorhabditis elegans, but the effects appear to be complex and the underlying mechanism for lifespan regulation by mitochondrial respiratory genes is still not fully understood. Here, we investigated the role of Y82E9BR.3, a worm homolog of the ATP synthase subunit C, in modulating longevity in C. elegans. We found that the Y82E9BR.3 protein is localized in mitochondria and expressed in various tissues throughout development. RNAi knockdown of Y82E9BR.3 extends lifespan, decreases the accumulation of lipofuscin, and affects various physiological processes, including development delay, reproduction impairment and slow behavior. Further tissue-specific RNAi analysis showed that the intestine is a crucial organ for the longevity effects conferred by Y82E9BR.3 RNAi. Moreover, we demonstrated that lifespan extension by Y82E9BR.3 RNAi is associated with reduced mitochondrial function, as well as the suppression of complex I activity in mitochondria. Unexpectedly, Y82E9BR.3 RNAi knock down did not influence the whole-worm ATP level. Our findings first reveal the crucial role of Y82E9BR.3 in mitochondrial function and the underlying mechanism of how Y82E9BR.3 regulates lifespan in C. elegans.
Changing environments during the Middle-Upper Palaeolithic transition in the eastern Cantabrian Region (Spain): direct evidence from stable isotope studies on ungulate bones
Authors: Jones Jennifer R. , Richards Michael P. , Straus Lawrence G. , Reade Hazel , Altuna Jesús , Mariezkurrena Koro , Marín-Arroyo Ana B. 
Published: September 2018

AbstractEnvironmental change has been proposed as a factor that contributed to the extinction of the Neanderthals in Europe during MIS3. Currently, the different local environmental conditions experienced at the time when Anatomically Modern Humans (AMH) met Neanderthals are not well known. In the Western Pyrenees, particularly, in the eastern end of the Cantabrian coast of the Iberian Peninsula, extensive evidence of Neanderthal and subsequent AMH activity exists, making it an ideal area in which to explore the palaeoenvironments experienced and resources exploited by both human species during the Middle to Upper Palaeolithic transition. Red deer and horse were analysed using bone collagen stable isotope analysis to reconstruct environmental conditions across the transition. A shift in the ecological niche of horses after the Mousterian demonstrates a change in environment, towards more open vegetation, linked to wider climatic change. In the Mousterian, Aurignacian and Gravettian, high inter-individual nitrogen ranges were observed in both herbivores. This could indicate that these individuals were procured from areas isotopically different in nitrogen. Differences in sulphur values between sites suggest some variability in the hunting locations exploited, reflecting the human use of different parts of the landscape. An alternative and complementary explanation proposed is that there were climatic fluctuations within the time of formation of these archaeological levels, as observed in pollen, marine and ice cores.
Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes
Authors: Günther Babett , Knebelsberger Thomas , Neumann Hermann , Laakmann Silke , Martínez Arbizu Pedro 
Published: September 2018

AbstractWe establish the new approach of environmental DNA (eDNA) analyses for the North Sea. Our study uses a multigene approach, including the mitochondrial cytochrome-c-oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity. A new minibarcode primer (124 bp) was created on the basis of a metazoan COI barcode library with 506 species and testedin silico,in vitro, andin situ. We applied high throughput sequencing to filtrates of 23 near-bottom water samples taken at three seasons from 14 stations. The set of COI primers allowed amplification of mitochondrial minibarcodes for diverse metazoan phyla and the differentiation at the species level for more than 99% of the specimens in the dataset. Our results revealed that the number of sequences is not consistent with proportions in the given DNA mixture. Altogether, environmental sequences could be assigned to 114 species and to 12 metazoan phyla. A spatial distribution of taxa recovered by eDNA was congruent with known distributions. Finally, the successful detection of species and biodiversity depends on a comprehensive sequence reference database. Our study offers a powerful tool for future biodiversity research, including the detection of nonnative species.
Two Engineered OBPs with opposite temperature-dependent affinities towards 1-aminoanthracene
Authors: Gonçalves Filipa , Castro Tarsila G. , Azoia Nuno G. , Ribeiro Artur , Silva Carla , Cavaco-Paulo Artur 
Published: September 2018

AbstractEngineered odorant-binding proteins (OBPs) display tunable binding affinities triggered by temperature alterations. We designed and produced two engineered proteins based on OBP-I sequence: truncated OBP (tOBP) and OBP::GQ20::SP-DS3. The binding affinity of 1-aminoanthracene (1-AMA) to these proteins revealed that tOBP presents higher affinity at 25 °C (kd = 0.45 μM) than at 37 °C (kd = 1.72 μM). OBP::GQ20::SP-DS3 showed an opposite behavior, revealing higher affinity at 37 °C (kd = 0.58 μM) than at 25 °C (kd = 1.17 μM). We set-up a system containing both proteins to evaluate their temperature-dependent binding. Our data proved the 1-AMA differential and reversible affinity towards OBPs, triggered by temperature changes. The variations of the binding pocket size with temperature, confirmed by molecular modelling studies, were determinant for the differential binding of the engineered OBPs. Herein we described for the first time a competitive temperature-dependent mechanism for this class of proteins.
Ultra-wide-band structural slow light
Authors: Lai Yiming , Mohamed Mohamed Sabry , Gao Boshen , Minkov Momchil , Boyd Robert W. , Savona Vincenzo , Houdré Romuald , Badolato Antonio 
Published: September 2018

AbstractThe ability of using integrated photonics to scale multiple optical components on a single monolithic chip offers key advantages to create miniature light-controlling chips. Numerous scaled optical components have been already demonstrated. However, present integrated photonic circuits are still rudimentary compared to the complexity of today’s electronic circuits. Slow light propagation in nanostructured materials is a key component for realizing chip-integrated photonic devices controlling the relative phase of light and enhancing optical nonlinearities. We present an experimental record high group-index-bandwidth product (GBP) of 0.47 over a 17.7 nm bandwidth in genetically optimized coupled-cavity-waveguides (CCWs) formed by L3 photonic crystal cavities. Our structures were realized in silicon-on-insulator slabs integrating up to 800 coupled cavities, and characterized by transmission, Fourier-space imaging of mode dispersion, and Mach-Zehnder interferometry.
Influence of water quality on diversity and composition of fungal communities in a tropical river
Authors: Ortiz-Vera Mabel Patricia , Olchanheski Luiz Ricardo , da Silva Eliane Gonçalves , de Lima Felipe Rezende , Martinez Lina Rocío del Pilar Rada , Sato Maria Inês Zanoli , Jaffé Rodolfo , Alves Ronnie , Ichiwaki Simone , Padilla Gabriel , Araújo Welington Luiz 
Published: September 2018

AbstractFreshwater fungi are key decomposers of organic material and play important roles in nutrient cycling, bio-remediation and ecosystem functioning. Although aquatic fungal communities respond to pollution, few studies have quantitatively assessed the effect of freshwater contamination on fungal diversity and composition; and knowledge is scarcer for tropical systems. Here we help fill this knowledge gap by studying a heavily-contaminated South American river spanning a biodiversity hotspot. We collected 30 water samples scattered across a quality gradient over two seasons and analyzed them using Terminal Restriction Fragment Length Polymorphisms (T-RFLP) coupled with 454 Pyrosequencing. Using T-RFLP we identified 451 and 442 Operational Taxonomy Units (OTUs) in the dry and rainy seasons respectively, whereas Pyrosequencing revealed 48,553 OTUs from which 11% were shared between seasons. Although 68% of all identified OTUs and 51% of all identified phyla remained unidentified, dominant fungal phyla included the Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota, Zygomycota and Neocallimastigomycota, whileCalcarisporiella,Didymosphaeria,Mycosphaerella(Ascomycota) andRhodotorula(Basidiomycota) were the most abundant genera. Fungal diversity was affected by pH and dissolved iron, while community composition was influenced by dissolved oxygen, pH, nitrate, biological oxygen demand, total aluminum, total organic carbon, total iron and seasonality. The presence of potentially pathogenic species was associated with high pH. Furthermore, geographic distance was positively associated with community dissimilarity, suggesting that local conditions allowed divergence among fungal communities. Overall, our findings raise potential concerns for human health and the functioning of tropical river ecosystems and they call for improved water sanitation systems.
FGF-7 Dictates Osteocyte Cell Processes Through Beta-Catenin Transduction
Authors: Liu Xiao-Yu , Li Xin , Bai Ming-Ru , Chen Xia , Wang Cheng-Lin , Xie Jing , Ye Ling 
Published: September 2018

AbstractIt is well recognized that osteocytes communicate with each other via gap junctions and that connxin43 (Cx43) shows its great potential in gap junction for the contribution enabling transmission of small molecules and operating in an autocrine/a paracrine manner. Fibroblast growth factors (FGFs) play significant roles in new bone formation and adult bone remodeling, and FGF signaling is regulated by the precise spatiotemporal approaches. However, the influence of FGF7 on osteocyte cell processes is not well elucidated. In this study, we aimed to examine the impact of FGF7 on osteocyte cell processes by characterizing the expression of Cx43 and to reveal the underlying mechanism regulating this cell process. We first found that the mRNA level of FGF7 was higher relative to other FGF family members both in osteocytes cell line (MLO-Y4) and bone tissue. We then demonstrated that FGF7 could increase the expression of Cx43 in osteocytes and promote the cell processes in the form of gap junctions between osteocytes. This modulation was due to the FGF7-induced cytoplasmic accumulation and resultant nuclear translocation of β-catenin. Our results could help us to further understand the importance of FGF7 on bone cell behavior and bone physiology and even pathology.
Ex vivo assessment and in vivo validation of non-invasive stent monitoring techniques based on microwave spectrometry
Authors: Gálvez-Montón Carolina , Arauz-Garofalo Gianluca , Rodriguez-Leor Oriol , Soler-Botija Carolina , Amorós García de Valdecasas Susana , Gerez-Britos Flavio David , Bayes-Genis Antoni , O’Callaghan Juan Manuel , Macià Ferran , Tejada Javier 
Published: September 2018

AbstractSome conditions are well known to be directly associated with stent failure, including in-stent re-occlusion and stent fracture. Currently, identification of these high-risk conditions requires invasive and complex procedures. This study aims to assess microwave spectrometry (MWS) for monitoring stents non-invasively. Preliminary ex vivo data are presented to move to in vivo validation. Fifteen mice were assigned to receive subcutaneous stent implantations (n = 10) or sham operations (n = 5). MWS measurements were carried out at 0, 2, 4, 7, 14, 22, and 29 days of follow-up. Additionally, 5 stented animals were summited to micro-CT analyses at the same time points. At 29 days, 3 animals were included into a stent fracture subgroup and underwent a last MWS and micro-CT analysis. MWS was able to identify stent position and in-stent stenosis over time, also discerning significant differences from baseline measures (P < 0.001). Moreover, MWS identified fractured vs. non-fractured stents in vivo. Taken together, MWS emerges as a non-invasive, non-ionizing alternative for stent monitoring. MWS analysis clearly distinguished between in-stent stenosis and stent fracture phenomena.
Combined Presigmoid and Retrosigmoid Approach to Petroclival Meningiomas
Authors: Rassi Marcio , Zamponi Johnni , Cândido Duarte , Oliveira Jean , Passos Gustavo , Borba Luis 
Published: September 2018

Introduction The management of petroclival meningiomas is among the most intimidating in neurosurgery, due to its difficult accessibility and close relationship with vital structures; therefore, an appropriate exposure is mandatory. We present a surgical video demonstrating a presigmoid transtentorial approach, associated with the opening of the retrosigmoid dura to a petroclival meningioma, performed by the senior surgeon (L.A.B.B.), along with its indications and pitfalls.
Approach Decision The patient's clinical history is summed to the tumor's radiological features as its extension, vascularization, and venous drainage, when selecting the appropriate approach. The presigmoid transtentorial approach offers a wide exposure of the petroclival area along with the tumor's attachment. Its association with the retrosigmoid route allows the surgeon to freely work through multiple paths, and parallel to the skull base, reducing the traction in the temporal lobe.
Clinical Case This is a 39-year-old female presenting with trigeminal neuralgia. Imaging depicted a petroclival meningioma, extending from the posterior aspect of the cavernous sinus to the cerebellopontine angle, extending inferiorly to the jugular bulb. A Simpson II resection was achieved through a combined presigmoid and retrosigmoid approach, and the patient was discharged with no complications or new deficits.
Conclusion Petroclival meningiomas are a formidable and surgically treatable disease. The appropriate approach is design to each patient and should not be the limiting factor for total tumor removal, which is truly given by the absence of a dissection plane between the tumor and the brainstem, nerves and vascular structures of the skull base.The link to the video can be found at: https://youtu.be/MFjqZvElBSo.
Designing effective public participation
Authors: Bobbio Luigi 
Published: September 2018

AbstractThis paper reviews the various connections that can exist between the design of participatory processes and the different kind of results that they can entail. It details how effective participatory processes can be designed, whatever are the results that participation is deemed to elicit. It shows the main trends pertaining to design choicesand considers how to classify different arrangements in order to choose from among them. Then the paper deals with the main dilemmas that tend to arise when designing participatory processes. Thanks to this review, the paper argues that participatory processes tend to display a certain degree of ambivalence that cannot be completely overcome through the design choices.
Learning and Imputation for Mass-spec Bias Reduction (LIMBR)
Authors: Crowell Alexander M , Greene Casey S , Loros Jennifer J , Dunlap Jay C 
Published: September 2018

Abstract

Motivation
Decreasing costs are making it feasible to perform time series proteomics and genomics experiments with more replicates and higher resolution than ever before. With more replicates and time points, proteome and genome-wide patterns of expression are more readily discernible. These larger experiments require more batches exacerbating batch effects and increasing the number of bias trends. In the case of proteomics, where methods frequently result in missing data this increasing scale is also decreasing the number of peptides observed in all samples. The sources of batch effects and missing data are incompletely understood necessitating novel techniques.

Results
Here we show that by exploiting the structure of time series experiments, it is possible to accurately and reproducibly model and remove batch effects. We implement Learning and Imputation for Mass-spec Bias Reduction (LIMBR) software, which builds on previous block-based models of batch effects and includes features specific to time series and circadian studies. To aid in the analysis of time series proteomics experiments, which are often plagued with missing data points, we also integrate an imputation system. By building LIMBR for imputation and time series tailored bias modeling into one straightforward software package, we expect that the quality and ease of large-scale proteomics and genomics time series experiments will be significantly increased.

Availability and implementation
Python code and documentation is available for download at https://github.com/aleccrowell/LIMBR and LIMBR can be downloaded and installed with dependencies using ‘pip install limbr’.

Supplementary information
Supplementary data are available at Bioinformatics online.