bluuebunny/crossref_metadata_2025_split huggingface dataset:
Projected amplification of food web bioaccumulation of MeHg and PCBs under climate change in the Northeastern Pacific
Authors: Alava Juan José , Cisneros-Montemayor Andrés M. , Sumaila U. Rashid , Cheung William W. L. 
Published: September 2018

AbstractClimate change increases exposure and bioaccumulation of pollutants in marine organisms, posing substantial ecophysiological and ecotoxicological risks. Here, we applied a trophodynamic ecosystem model to examine the bioaccumulation of organic mercury (MeHg) and polychlorinated biphenyls (PCBs) in a Northeastern Pacific marine food web under climate change. We found largely heterogeneous sensitivity in climate-pollution impacts between chemicals and trophic groups. Concentration of MeHg and PCBs in top predators, including resident killer whales, is projected to be amplified by 8 and 3%, respectively, by 2100 under a high carbon emission scenario (Representative Concentration Pathway 8.5) relative to a no-climate change control scenario. However, the level of amplification increases with higher carbon emission scenario for MeHg, but decreases for PCBs. Such idiosyncratic responses are shaped by the differences in bioaccumulation pathways between MeHg and PCBs, and the modifications of food web dynamics between different levels of climate change. Climate-induced pollutant amplification in mid-trophic level predators (Chinook salmon) are projected to be higher (~10%) than killer whales. Overall, the predicted trophic magnification factor is ten-fold higher in MeHg than in PCBs under high CO2 emissions. This contribution highlights the importance of understanding the interactions with anthropogenic organic pollutants in assessing climate risks on marine ecosystems.
Organizational principles of multidimensional predictions in human auditory attention
Authors: Wollman Indiana , Morillon Benjamin 
Published: September 2018

AbstractAnticipating the future rests upon our ability to exploit contextual cues and to formulate valid internal models or predictions. It is currently unknown how multiple predictions combine to bias perceptual information processing, and in particular whether this is determined by physiological constraints, behavioral relevance (task demands), or past knowledge (perceptual expertise). In a series of behavioral auditory experiments involving musical experts and non-musicians, we investigated the respective and combined contribution of temporal and spectral predictions in multiple detection tasks. We show that temporal and spectral predictions alone systematically increase perceptual sensitivity, independently of task demands or expertise. When combined, however, spectral predictions benefit more to non-musicians and dominate over temporal ones, and the extent of the spectrotemporal synergistic interaction depends on task demands. This suggests that the hierarchy of dominance primarily reflects the tonotopic organization of the auditory system and that expertise or attention only have a secondary modulatory influence.
High abundances of the nuisance raphidophyte Gonyostomum semen in brown water lakes are associated with high concentrations of iron
Authors: Lebret Karen , Östman Örjan , Langenheder Silke , Drakare Stina , Guillemette François , Lindström Eva S. 
Published: September 2018

AbstractAlgal blooms occur frequently in lakes and oceans and the causes and consequences of those are often studied. In this study, we focus on a less well known type of algal bloom by the freshwater raphidophyte Gonyostomum semen. This species’ abundance and occurrence is increasing, especially in brown water lakes, the most abundant lake type in the boreal zone. The aim of the study was to investigate which environmental factors are associated with G. semen by statistical evaluation of field data of 95 Swedish lakes over five years. Although we found G. semen to be associated with dark waters it was, contrary to our expectations, mainly high concentrations of iron, and only to a lesser extent high TOC (total organic carbon) concentrations, that were associated with blooms of G. semen. In addition, high phosphorus concentrations and low pH also appear to facilitate G. semen blooms. We suggest that browning of lakes caused by increased iron concentrations may decrease net heterotrophy by fostering heavy algal blooms, i.e. the opposite to commonly assumed effects of increased DOM (dissolved organic matter).
Measuring the Wilson depression of sunspots using the divergence-free condition of the magnetic field vector
Authors: Löptien B. , Lagg A. , van Noort M. , Solanki S. K. 
Published: September 2018

Context. The Wilson depression is the difference in geometric height of unit continuum optical depth between the sunspot umbra and the quiet Sun. Measuring the Wilson depression is important for understanding the geometry of sunspots. Current methods suffer from systematic effects or need to make assumptions on the geometry of the magnetic field. This leads to large systematic uncertainties of the derived Wilson depressions.
Aims. We aim to develop a robust method for deriving the Wilson depression that only requires the information about the magnetic field that is accessible from spectropolarimetry, and that does not rely on assumptions on the geometry of sunspots or on their magnetic field.
Methods. Our method is based on minimizing the divergence of the magnetic field vector derived from spectropolarimetric observations. We have focused on large spatial scales only in order to reduce the number of free parameters.
Results. We tested the performance of our method using synthetic Hinode data derived from two sunspot simulations. We find that the maximum and the umbral averaged Wilson depression for both spots determined with our method typically lies within 100 km of the true value obtained from the simulations. In addition, we applied the method to Hinode observations of a sunspot. The derived Wilson depression (∼600 km) is consistent with results typically obtained from the Wilson effect. We also find that the Wilson depression obtained from using horizontal force balance gives 110–180 km smaller Wilson depressions than both, what we find and what we deduce directly from the simulations. This suggests that the magnetic pressure and the magnetic curvature force contribute to the Wilson depression by a similar amount.
Plötzlicher, unerwarteter Tod bei Epilepsie: Mechanismen und Prävention
Authors: Pensel Max , Surges Rainer 
Published: September 2018

ZusammenfassungSUDEP ist ein Akronym aus dem Englischen (sudden, unexpected death in epilepsy) und benennt den plötzlichen, unerwarteten Tod von Menschen mit Epilepsie. Es handelt sich um eine seltene, aber gravierende Gefahr für Epilepsiepatienten. Im Folgenden soll gezeigt werden, welche Mechanismen und Risikofaktoren eine Rolle spielen und wie das Auftreten von SUDEP verhindert werden kann.
Neuroimaging in Autoimmune and Neuroinflammation-Related Epilepsies
Authors: Altinok Deniz , Kumar Ajay , Saleem Sheena 
Published: September 2018

AbstractAutoimmune encephalitis is increasingly recognized as a cause of new onset altered mental status and seizures with a wide range of neuroimaging findings. We will describe the neuroimaging findings in autoimmune and neuroinflammation-related epilepsies.
Biomechanical Responses of Neonatal Brachial Plexus to Mechanical Stretch
Authors: Singh Anita , Shaji Shania , Delivoria-Papadopoulos Maria , Balasubramanian Sriram 
Published: September 2018

AbstractThis study investigated the biomechanical responses of neonatal piglet brachial plexus (BP) segments—root/trunk, chord, and nerve at two different rates, 0.01 mm/second (quasistatic) and 10 mm/second (dynamic)—and compared their response to another peripheral nerve (tibial). Comparisons of mechanical responses at two different rates reported a significantly higher maximum load, maximum stress, and Young's modulus (E) values when subjected to dynamic rate. Among various BP segments, maximum stress was significantly higher in the nerve segments, followed by chord and then the root/trunk segments except no differences between chord and root/trunk segments at quasistatic rate. E values exhibited similar behavior except no differences between the chord and root/trunk segments at both rates and no differences between chord and nerve segments at quasistatic rate. No differences were observed in the strain values. When compared with the tibial nerve, only mechanical properties of BP nerves were similar to the tibial nerve. Mechanical stresses and E values reported in BP root/trunk and chord segments were significantly lower than tibial nerve at both rates. When comparing the failure pattern, at quasistatic rate, necking was observed at maximum load, before a complete rupture occurred. At dynamic rate, partial rupture at maximum load, followed by a full rupture, was observed. Occurrence of the rate-dependent failure phenomenon was highest in the root/trunk segments followed by chord and nerve segments. Differences in the maximum stress, E values, and failure pattern of BP segments confirm variability in their anatomical structure and warrant future histological studies to better understand their stretch responses.
Novel Interpositional Vein Grafting for Pedicle Extension of Island Pedicle Flaps
Authors: Yoshida Shuhei , Koshima Isao , Nagamatsu Shogo , Yokota Kazunori , Yamashita Shuji , Harima Mitsunobu , Tashiro Kensuke 
Published: September 2018

Background Island pedicle flaps often have the problem of limited reach. In such cases, free flaps are useful for reconstruction but often have the issue of unavailability of suitable recipient vessels. Therefore, it would be helpful if the pedicle of an island flap could be extended as far as necessary.
Methods Here, we describe the use of interpositional vein grafts to extend island pedicle flaps for the reconstruction of an ischemic above-knee amputation stump in one case and to seal an intractable fistula on the buttock after radiation therapy in another case. In the patient with the ischemic stump, a deep inferior epigastric perforator flap was extended by 6 cm using the great saphenous vein harvested from the contralateral side, allowing successful coverage of the stump. In the patient with an intractable fistula on the buttock, a thoracodorsal artery and vein graft that was extended by 25 cm using the cephalic vein harvested from the right forearm to upper arm allowed successful sealing of the fistula.
Results Circulation was satisfactory in both cases and both flaps survived. The operative procedure was straightforward.
Conclusion Interpositional vein grafts may be a feasible option for the extension of island pedicle flaps to include the features of an island pedicle flap and a free flap.
Analysis of the Anti-Inflammatory Potential of Pure and Microemulsified Bullfrog Oil in Acute Lung Injury
Authors: Davim André , Dantas Tereza , Pereira Márcia 
Published: September 2018

AbstractInfectious diseases account for more than a third of all hospital admissions, and are highly prevalent in intensive care units. Currently, sepsis is one of the diseases with the highest morbidity and mortality rates worldwide, with death rates reaching up to 60% among intensive care patients, according to statistics from low-income countries. The prominence of multi-resistant microorganisms is rising, while the possibilities of development of new target drugs are being exhausted. Thus, the objective of the present study was to evaluate the anti-inflammatory potential of bullfrog oil in its pure state and in a microemulsion system in an experimental model of sepsis. Mice were separated into three groups and treated with bullfrog oil in its pure state, in a microemulsion, and with saline solution, and subsequently submitted to induction of sepsis. Bronchoalveolar lavages were performed for cell counts, as well as analyses of lung tissue samples. When the washings were analyzed, no statistically significant difference was observed in cell migration between the experimental groups, but a difference was observed between these groups and the saline solution group. When the lung tissue samples were analyzed, intense tissue wear was observed in the bullfrog oil groups, with the presence of cellular infiltrate and rupture of respiratory bronchioles and alveoli. However, in the microemulsion group, no major tissue wear was observed, and the pulmonary parenchyma was more preserved. Thus, we concluded that bullfrog oil in pure form and in a microemulsion system are good modulators of the inflammatory response, with the microemulsion system being more efficient in protecting lung tissue.
Strain Elastography: A Valuable Additional Method to BI-RADS?
Authors: Zhao Xin-Bao , Yao Ji-Yi , Zhou Xin , Hao Shao-Yun , Mu Wen , Li Lu-Jing , Zhong Wen-Jing , Hui Zhi 
Published: September 2018

Abstract
Background Breast lesions classified as BI-RADS-US 3 are probably benign and observation was recommended, while a considerable number of BI-RADS-US 4 lesions were benign, resulting in excessive biopsies. We focus exclusively on BI-RADS-US 3 and 4 lesions and hypothesize that improved diagnostic performance can be achieved by integrating real-time elastography (strain ratio) into the BI-RADS-US classification system.
Method From April 2010 to September 2015, 1071 lesions were included in the final analysis. After the conventional ultrasound examination, the BI-RADS-US (2013) classification was used to evaluate the lesions. Then the strain ratios were calculated, and the final diagnosis was made on the basis of histological results. The sensitivity, specificity, accuracy, PPV and NPV were calculated and the AUCs were compared. Additionally, an analysis of the diagnostic performance expressed by the pretest and posttest probability of disease (POD) was performed in BI-RADS-US 3 and 4A lesions.
Results With the cutoff point of 2.98, the sensitivity, specificity and accuracy of the strain ratio method were 86.9 %, 86.6 % and 82.6 %, respectively. In BI-RADS-US 3 lesions, a suspicious strain ratio significantly modified the POD from 1.3 % to a posttest POD of 29.8 %. In BI-RADS-US 4A lesions, a suspicious strain ratio significantly modified the POD from 8.5 % to a posttest POD of 48.7 %.
Conclusion Ultrasonographic elastography (strain ratio) yields additional diagnostic information in the evaluation of BI-RADS-US 3 and 4 breast lesions. The strain ratios should be integrated into the BI-RADS-US classification system and into daily practice.
Interpreting cognitive decline in the face of cognitive reserve
Authors: Bialystok Ellen , Anderson John A. E. , Grundy John G. 
Published: September 2018

Abstract
Evaluation of the cognitive level of older adults, including decisions about meeting clinical thresholds for dementia, is typically based on behavioral levels of performance. However, individuals with high cognitive reserve will outperform the levels typically associated with their brain structure, providing inaccurate assessments of their status. We define cognitive reserve as the relation between brain integrity and cognitive level, and use the case of bilingualism as a source of cognitive reserve to illustrate how information from only one can distort the interpretation of the individual’s cognitive status.
AGILE: an assembled genome mining pipeline
Authors: Hughes Graham M , Teeling Emma C 
Published: September 2018

Abstract

Summary
A number of limiting factors mean that traditional genome annotation tools either fail or perform sub-optimally when trying to detect coding sequences in poor quality genome assemblies/genome reports. This means that potentially useful data is accessible only to those with specific skills and expertise in assembly and annotation. We present an Assembled-Genome mIning pipeLinE (AGILE) written in Perl that combines bioinformatics tools with a number of steps to overcome the limitations imposed by such assemblies when applied to highly fragmented genomes. Our methodology uses user-specified query genes from a closely related species to mine and annotate coding sequences that would traditionally be missed by standard annotation packages. Despite a focus on mammalian genomes, the generalized implementation means that it may be applied to any genome assembly, providing a means for non-specialists to gather gene sequences for downstream analyses.

Availability and implementation
Source code and associated files are available at: https://github.com/batlabucd/GenomeMining and https://bitbucket.org/BatlabUCD/genomemining/src. Singularity and Virtual Box images available at https://figshare.com/s/a0004bf93dc43484b0c0.

Supplementary information
Supplementary data are available at Bioinformatics online.
Molecular differential diagnosis of uterine leiomyomas and leiomyosarcomas
Authors: Mas Aymara , Simón Carlos 
Published: September 2018

Abstract
Uterine leiomyomas (LM) and leiomyosarcomas (LMS) are considered biologically unrelated tumors due to their cytogenetic and molecular disparity. Yet, these tumors share morphological and molecular characteristics that cannot be differentiated through current clinical diagnostic tests, and thus cannot be definitively classified as benign or malignant until surgery. Newer approaches are needed for the identification of these tumors, as has been done for other tissues. The application of next generation sequencing enables the detection of new mutations that, when coupled to machine learning bioinformatic tools, advances our understanding of chromosomal instability. These approaches in the context of LM and LMS could allow the discovery of genetic variants and possible genomic markers. Additionally, the potential clinical utility of circulating cell-free tumor DNA could revolutionize the noninvasive detection and monitoring of these tumors. Here, we seek to provide a perspective on the molecular background of LM and LMS, recognizing their distinct molecular features that may lead to improved diagnosis and personalized treatments, which would have a measurable impact on women's reproductive health.
The Herschel-PACS North Ecliptic Pole Survey
Authors: Pearson Chris , Barrufet Laia , Campos Varillas Maria del Carmen , Serjeant Stephen , Clements David L , Goto Tomotsugu , Im Myungshin , Jeong Woong-Seob , Kim Seong Jin , Matsuhara Hideo , Sedgwick Chris , Valtchanov Ivan 
Published: September 2018

Abstract
A detailed analysis of Herschel/Photoconductor Array Camera and Spectrometer (PACS) observations at the North Ecliptic Pole is presented. High-quality maps, covering an area of 0.44 deg2, are produced and then used to derive potential candidate source lists. A rigorous quality-control pipeline has been used to create final legacy catalogues in the PACS Green 100 μm and Red 160 μm bands, containing 1384 and 630 sources respectively. These catalogues reach to more than twice the depth of the current archival Herschel/PACS Point Source Catalogue, detecting 400 and 270 more sources in the short- and long-wavelength bands, respectively. Galaxy source counts are constructed that extend down to flux densities of 6 mJy and 19 mJy (50% completeness) in the Green 100 μm and Red 160 μm bands, respectively. These source counts are consistent with previously published PACS number counts in other fields across the sky. The source counts are then compared with a galaxy evolution model which identifies a population of luminous infrared galaxies as responsible for the bulk of the galaxy evolution over the flux range (5–100 mJy) spanned by the observed counts, contributing approximate fractions of 50% and 60% to the cosmic infrared background at 100 μm and 160 μm, respectively.
Genomic, transcriptomic, and structural analysis ofPseudomonasvirus PA5oct highlights the molecular complexity among Jumbo phages
Authors: Danis-Wlodarczyk Katarzyna , Blasdel Bob G. , Jang Ho Bin , Vandenheuvel Dieter , Noben Jean-Paul , Drulis-Kawa Zuzanna , Lavigne Rob 
Published: September 2018

AbstractPseudomonasvirus PA5oct has a large, linear, double-stranded DNA genome (287,182 bp) and is related toEscherichiaphages 121Q/PBECO 4,Klebsiellaphage vB_KleM-RaK2,Klebsiellaphage K64-1, andCronobacterphage vB_CsaM_GAP32. A protein-sharing network analysis highlights the conserved core genes within this clade. Combining genome, RNAseq and mass spectrometry analyses of its virion proteins allowed us to accurately identify genes and elucidate regulatory elements for this phage (ncRNAs, tRNAs and promoter elements). In total PA5oct encodes 462 CDS (compared to 345in silicopredicted genes using automated annotation pipelines), of which 25.32%, have been identified as virion-associated based on ESI-MS/MS. The RNAseq-based temporal genome organization suggests a gradual take-over by viral transcripts from 21%, 69%, and 92% at 5, 15 and 25 min after infection, respectively. Like many large phages, PA5oct is not organized into contiguous regions of temporal transcription. However, although the temporal regulation of the PA5oct genome expression reveals specific genome clusters expressed in early and late infection, many genes encoding experimentally observed structural proteins surprisingly appear to remain almost untranscribed throughout the infection cycle. Within the host, operons associated with elements of a cryptic Pf1-like prophage are upregulated, as are operons responsible for Psl exopolysaccharide (pslE-J) and periplasmic nitrate reductase (napA-F) production. The characterization described here represents a crucial step towards understanding the genomic complexity as well as molecular diversity of jumbo viruses.
Microinjection into theCaenorhabditis elegansembryo using an uncoated glass needle enables cell lineage visualization and reveals cell-non-autonomous adhesion control
Authors: Kikuchi Yohei , Kimura Akatsuki 
Published: September 2018

AbstractMicroinjection is a useful method in cell biology, with which exogenous substances are introduced into a cell in a location- and time-specific manner. TheCaenorhabditis elegansembryo is an important model system for cell and developmental biology. Applying microinjection to theC. elegansembryo had been difficult due to the rigid eggshell surrounding the embryo. In 2013, microinjection method using a carbon-coated quartz needle for theC. elegansembryo was reported. To prepare the needle, unfortunately, special equipment is required and thus a limited number of researchers can use this method. In this study, we established a method for the microinjection of drugs, dyes, and microbeads into theC. elegansembryo using an uncoated glass needle that can be produced in a general laboratory. This method enabled us to easily detect cell lineage up to adult stages by injecting a fluorescent dye into a blastomere. We also found a cell-non-autonomous control mechanism of cell adhesion; specifically, the injection of an actin inhibitor into one cell at the 2-cell stage enhanced adhesion between daughter cells of the other cell. Our microinjection method is expected to be used for broad studies and could facilitate various discoveries usingC. elegans.