bluuebunny/crossref_metadata_2025_split huggingface dataset:
A diverse mammal-dominated, footprint assemblage from wetland deposits in the Lower Cretaceous of Maryland
Authors: Stanford Ray , Lockley Martin G. , Tucker Compton , Godfrey Stephen , Stanford Sheila M. 
Published: January 2018

AbstractA newly discovered assemblage of predominantly small tracks from the Cretaceous Patuxent Formation at NASA’s Goddard Space Flight Center, Maryland, reveals one of the highest track densities and diversities ever reported (~70 tracks, representing at least eight morphotypes from an area of only ~2 m2). The assemblage is dominated by small mammal tracks including the new ichnotxon Sederipes goddardensis, indicating sitting postures. Small crow-sized theropod trackways, the first from this unit, indicate social trackmakers and suggest slow-paced foraging behavior. Tracks of pterosaurs, and other small vertebrates suggest activity on an organic-rich substrate. Large well-preserved sauropod and nodosaurs tracks indicate the presence of large dinosaurs. The Patuxent Formation together with the recently reported Angolan assemblage comprise the world’s two largest Mesozoic mammal footprint assemblages. The high density of footprint registration at the NASA site indicates special preservational and taphonomic conditions. These include early, penecontemporaneous deposition of siderite in organic rich, reducing wetland settings where even the flesh of body fossils can be mummified. Thus, the track-rich ironstone substrates of the Patuxent Formation, appear to preserve a unique vertebrate ichnofacies, with associated, exceptionally-preserved body fossil remains for which there are currently no other similar examples preserved in the fossil record.
An engineered CARS substrate with giant field enhancement in crisscross dimer nanostructure
Authors: Zhang Jia , Chen Shu , Wang Junqiao , Mu Kaijun , Fan Chunzhen , Liang Erjun , Ding Pei 
Published: January 2018

AbstractWe theoretically investigate the optical properties of a nanostructure consisting of the two identical and symmetrically arranged crisscrosses. A plasmonic Fano resonance is induced by a strong interplay between bright mode and dark modes, where the bright mode is due to electric dipole resonance while dark modes originate from the magnetic dipole induced by LC resonances. In this article, we find that the electric field “hotspots” corresponding to three different wavelengths can be positioned at the same spatial position, and its spectral tunability is achieved by changing geometric parameters. The crisscrosses system can be designed as a plasmonic substrate for enhancing Coherent Anti-Stokes Raman Scattering (CARS) signal. This discovery provides a new method to achieve single molecule detection. At the same time, it also has many important applications for multi-photon imaging and other nonlinear optical processes, such as four-wave mixing and stimulated Raman scattering.
Novel analgesic effects of melanin-concentrating hormone on persistent neuropathic and inflammatory pain in mice
Authors: Jang Jae-Hwan , Park Ji-Yeun , Oh Ju-Young , Bae Sun-Jeong , Jang Hyunchul , Jeon Songhee , Kim Jongpil , Park Hi-Joon 
Published: January 2018

AbstractThe melanin-concentrating hormone (MCH) is a peptidergic neuromodulator synthesized by neurons in the lateral hypothalamus and zona incerta. MCHergic neurons project throughout the central nervous system, indicating the involvements of many physiological functions, but the role in pain has yet to be determined. In this study, we found that pMCH−/− mice showed lower baseline pain thresholds to mechanical and thermal stimuli than did pMCH+/+ mice, and the time to reach the maximum hyperalgesic response was also significantly earlier in both inflammatory and neuropathic pain. To examine its pharmacological properties, MCH was administered intranasally into mice, and results indicated that MCH treatment significantly increased mechanical and thermal pain thresholds in both pain models. Antagonist challenges with naltrexone (opioid receptor antagonist) and AM251 (cannabinoid 1 receptor antagonist) reversed the analgesic effects of MCH in both pain models, suggesting the involvement of opioid and cannabinoid systems. MCH treatment also increased the expression and activation of CB1R in the medial prefrontal cortex and dorsolateral- and ventrolateral periaqueductal grey. The MCH1R antagonist abolished the effects induced by MCH. This is the first study to suggest novel analgesic actions of MCH, which holds great promise for the application of MCH in the therapy of pain-related diseases.
Twelve thousand recent patellogastropods from a northeastern Pacific latitudinal gradient
Authors: Kahanamoku Sara S. , Hull Pincelli M. , Lindberg David R. , Hsiang Allison Y. , Clites Erica C. , Finnegan Seth 
Published: January 2018

AbstractBody size distributions can vary widely among communities, with important implications for ecological dynamics, energetics, and evolutionary history. Here we present a dataset of body size and shape for 12,035 extant Patellogastropoda (true limpet) specimens from the collections of the University of California Museum of Paleontology, compiled using a novel high-throughput morphometric imaging method. These specimens were collected over the past 150 years at 355 localities along a latitudinal gradient ranging from Alaska to Baja California, Mexico and are presented here with individual images, 2D outline coordinates, and 2D measurements of body size and shape. This dataset provides a resource for assemblage-scale macroecological questions and documents the size and diversity of recent patellogastropods in the northeastern Pacific.
Simulations of fully deformed oscillating flux tubes
Authors: Karampelas K. , Van Doorsselaere T. 
Published: January 2018

Context. In recent years, a number of numerical studies have been focusing on the significance of the Kelvin–Helmholtz instability in the dynamics of oscillating coronal loops. This process enhances the transfer of energy into smaller scales, and has been connected with heating of coronal loops, when dissipation mechanisms, such as resistivity, are considered. However, the turbulent layer is expected near the outer regions of the loops. Therefore, the effects of wave heating are expected to be confined to the loop’s external layers, leaving their denser inner parts without a heating mechanism. Aim. In the current work we aim to study the spatial evolution of wave heating effects from a footpoint driven standing kink wave in a coronal loop. Methods. Using the MPI-AMRVAC code, we performed ideal, three dimensional magnetohydrodynamic simulations of footpoint driven transverse oscillations of a cold, straight coronal flux tube, embedded in a hotter environment. We have also constructed forward models for our simulation using the FoMo code. Results. The developed transverse wave induced Kelvin–Helmholtz (TWIKH) rolls expand throughout the tube cross-section, and cover it entirely. This turbulence significantly alters the initial density profile, leading to a fully deformed cross section. As a consequence, the resistive and viscous heating rate both increase over the entire loop cross section. The resistive heating rate takes its maximum values near the footpoints, while the viscous heating rate at the apex. Conclusions. We conclude that even a monoperiodic driver can spread wave heating over the whole loop cross section, potentially providing a heating source in the inner loop region. Despite the loop’s fully deformed structure, forward modelling still shows the structure appearing as a loop.
The first ICRANet catalog of binary-driven hypernovae
Authors: Pisani G. B. , Ruffini R. , Aimuratov Y. , Bianco C. L. , Karlica M. , Kovacevic M. , Moradi R. , Muccino M. , Penacchioni A. V. , Primorac D. , Rueda J. A. , Wang Y. 
Published: January 2018

In a series of recent publications, scientists from ICRANet, led by professor Remo Ruffini, have reached a novel comprehensive picture of gamma-ray bursts (GRBs) thanks to their development of a series of new theoretical approaches. Among those, the induced gravitational collapse (IGC) paradigm explains a class of energetic, long-duration GRBs associated with Ib/c supernovae (SN), recently named binary-driven hypernovae (BdHNe).
BdHNe have a well defined set of observational features which allow to identify them. Among them, the main two are: 1) long duration of the GRB explosion, namely larger than 2 s in the rest frame; 2) a total energy, released in all directions by the GRB explosion, larger than 1052 ergs.
A striking result is the observation, in the BdHNe sources, of a universal late time power-law decay in the X-rays luminosity after 104 s, with typical decaying slope of ~ 1.5. This leads to the possible establishment of a new distance indicator having redshift up to z ~ 8.
Thanks to this novel theoretical and observational understanding, it was possible for ICRANet scientists to build the firstst BdHNe catalog, composed by the 345 BdHNe identified up to the end of 2016.
Impact of Surgical Margin in Skull Base Surgery for Head and Neck Sarcomas
Authors: Matsumoto Fumihiko , Miyakita Yasuji , Mori Taisuke , Shimoi Tatsunori , Murakami Naoya , Yoshida Akihiko , Arakawa Ayumu , Omura Go , Fukasawa Masahiko , Matsumoto Yoshifumi , Matsumura Satoko , Itami Jun , Narita Yoshitaka , Yoshimoto Seiichi , Kobayashi Kenya 
Published: January 2018

Objective This study aimed to determine the adequate resection margin in skull base surgery for head and neck sarcoma.
Design We retrospectively reviewed 22 sarcomas with skull base invasion. Induction chemotherapy, followed by surgery and postoperative radiotherapy and adjuvant chemotherapy, was performed in 18 patients with chemosensitive sarcomas, and surgery with or without postoperative radiotherapy was performed in four patients with chemoresistant sarcomas. Radical resection was performed in patients with chemosensitive sarcomas with a poor response to induction chemotherapy and in patients with chemoresistant sarcomas. Conservative resection with close surgical margin was performed in patients with chemosensitive sarcomas with a good response to induction chemotherapy.
Setting and Participants This single-centered retrospective study included patients from the National Cancer Center Hospital, Japan.
Results The response to induction chemotherapy was significantly associated with the 3-year local control rate (LCR; good response versus poor response: 100% versus 63%, p = 0.048). Patients with a good response to chemotherapy had a favorable local prognosis even when the local therapy was conservative resection. In radical skull base surgery, patients whose surgical margins were classified as “wide margin positive” had significantly poorer 3-year LCR than did patients with “margin negative” or “micro margin positive” margins (25% versus 83%, p = 0.014).
Conclusion Conservative resection with close surgical margins might be acceptable for chemosensitive sarcomas with a good response to chemotherapy. Resection margin status was an important predictive factor for local recurrence after radical skull base surgery. Microscopic microresidual tumor might be controlled by postoperative treatment.
Growth is required for perception of water availability to pattern root branches in plants
Authors: Robbins Neil E. , Dinneny José R. 
Published: January 2018

Significance
Plant roots activate lateral branching in response to contact with available water, but the mechanism by which this environmental signal is perceived is poorly understood. Through a combination of empirical and mathematical-modeling approaches we discovered a central role of tissue growth in this process. Growth causes water uptake, and the biophysical changes that occur during this process are interpreted by the organism to position new lateral branches. This observation is a significant advancement in our understanding of how the environment shapes plant development and demonstrates that perception of water is intimately tied to a core biological function of the root.
Dual evolutionary origin of insect wings supported by an investigation of the abdominal wing serial homologs in
Tribolium
Authors: Linz David M. , Tomoyasu Yoshinori 
Published: January 2018

Significance
Acquisition of morphologically novel structures can facilitate successful radiation during evolution. The emergence of wings in hexapods represents a profound moment in eukaryotic evolution, making insects one of the most successful groups. However, the tissue that gave rise to this novel and evolutionarily crucial structure, and the mechanism that facilitated its evolution, are still under intense debate. By studying various wing-related tissues in beetles, we demonstrated that two distinct lineages of wing-related tissues are present even outside the appendage-bearing segments. This outcome supports a dual evolutionary origin of insect wings, and shows that novelty can emerge through two previously unassociated tissues collaborating to form a new structure.
The social genome of friends and schoolmates in the National Longitudinal Study of Adolescent to Adult Health
Authors: Domingue Benjamin W. , Belsky Daniel W. , Fletcher Jason M. , Conley Dalton , Boardman Jason D. , Harris Kathleen Mullan 
Published: January 2018

Significance
Our study reported significant findings of a “social genome” that can be quantified and studied to understand human health and behavior. In a national sample of more than 5,000 American adolescents, we found evidence of social forces that act to make friends and schoolmates more genetically similar to one another compared with random pairs of unrelated individuals. This subtle genetic similarity was observed across the entire genome and at sets of genomic locations linked with specific traits—educational attainment and body mass index—a phenomenon we term “social–genetic correlation.” We also find evidence of a “social–genetic effect” such that the genetics of a person’s friends and schoolmates influenced their own education, even after accounting for the person’s own genetics.
Golgi stress response reprograms cysteine metabolism to confer cytoprotection in Huntington’s disease
Authors: Sbodio Juan I. , Snyder Solomon H. , Paul Bindu D. 
Published: January 2018

Significance
Golgi stress response is emerging as a major stress response pathway although molecular players in the process have not been identified. We show that Golgi stress response induced by the ionophore monensin is mediated by the PERK-ATF4 pathway. We further show that subtoxic levels of monensin precondition cells to respond to future damaging insults. Monensin stimulates the reverse transsulfuration pathway via cystathionine γ-lyase, the biosynthetic enzyme for cysteine, important for redox homeostasis. We have harnessed this pathway to mitigate toxicity associated with cysteine deprivation in Huntington’s disease (HD). These findings are relevant to not only HD, but also other diseases involving redox imbalance. Targeting the molecular controls for restoration of cysteine balance may offer more robust therapeutic avenues for disease management.
Key comparison BIPM.RI(I)-K1 of the air-kerma standards of the IST-LPSR, Portugal and the BIPM in 60Co gamma radiation
Authors: Kessler C , Burns D , Cardoso J 
Published: January 2018

A comparison of the standards for air kerma of the Instituto Superior Técnico, Laboratório de Proteção e Segurança Radiológica (IST-LPSR), Portugal and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 60Co radiation beam of the BIPM in December 2015. The comparison result, evaluated as a ratio of the IST-LPSR and the BIPM standards for air kerma, is 1.0026 with a combined standard uncertainty of 1.7 × 10−3. The results for an indirect comparison made at the same time are consistent with the direct results at the level of 1.1 parts in 103. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Enrichment analysis with EpiAnnotator
Authors: Pageaud Yoann , Plass Christoph , Assenov Yassen 
Published: January 2018

Abstract

Motivation
Deciphering relevant biological insights from epigenomic data can be a challenging task. One commonly used approach is to perform enrichment analysis. However, finding, downloading and using the publicly available functional annotations require time, programming skills and IT infrastructure. Here we describe the online tool EpiAnnotator for performing enrichment analyses on epigenomic data in a fast and user-friendly way.

Results
EpiAnnotator is an R Package accompanied by a web interface. It contains regularly updated annotations from 4 public databases: Blueprint, RoadMap, GENCODE and the UCSC Genome Browser. Annotations are hosted locally or in a server environment and automatically updated by scripts of our own design. Thousands of tracks are available, reflecting data on a variety of tissues, cell types and cell lines from the human and mouse genomes. Users need to upload sets of selected and background regions. Results are displayed in customizable and easily interpretable figures.

Availability and implementation
The R package and Shiny app are open source and available under the GPL v3 license. EpiAnnotator’s web interface is accessible at http://computational-epigenomics.com/en/epiannotator.
Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms
Authors: Ferraro Petrillo Umberto , Roscigno Gianluca , Cattaneo Giuseppe , Giancarlo Raffaele 
Published: January 2018

AbstractMotivationInformation theoretic and compositional/linguistic analysis of genomes have a central role in bioinformatics, even more so since the associated methodologies are becoming very valuable also for epigenomic and meta-genomic studies. The kernel of those methods is based on the collection of k-mer statistics, i.e. how many times each k-mer in {A,C,G,T}k occurs in a DNA sequence. Although this problem is computationally very simple and efficiently solvable on a conventional computer, the sheer amount of data available now in applications demands to resort to parallel and distributed computing. Indeed, those type of algorithms have been developed to collect k-mer statistics in the realm of genome assembly. However, they are so specialized to this domain that they do not extend easily to the computation of informational and linguistic indices, concurrently on sets of genomes.ResultsFollowing the well-established approach in many disciplines, and with a growing success also in bioinformatics, to resort to MapReduce and Hadoop to deal with ‘Big Data’ problems, we present KCH, the first set of MapReduce algorithms able to perform concurrently informational and linguistic analysis of large collections of genomic sequences on a Hadoop cluster. The benchmarking of KCH that we provide indicates that it is quite effective and versatile. It is also competitive with respect to the parallel and distributed algorithms highly specialized to k-mer statistics collection for genome assembly problems. In conclusion, KCH is a much needed addition to the growing number of algorithms and tools that use MapReduce for bioinformatics core applications.Availability and implementationThe software, including instructions for running it over Amazon AWS, as well as the datasets are available at http://www.di-srv.unisa.it/KCH.Supplementary informationSupplementary data are available at Bioinformatics online.
Frontoparietal Activity Interacts With Task-Evoked Changes in Functional Connectivity
Authors: Hwang Kai , Shine James M , D’Esposito Mark 
Published: January 2018

Abstract
Flexible interactions between brain regions enable neural systems to adaptively transfer and process information. However, the neural substrates that regulate adaptive communications between brain regions are understudied. In this human fMRI study, we investigated this issue by tracking time-varying, task-evoked changes in functional connectivity between localized occipitotemporal regions while participants performed different tasks on the same visually presented stimuli. We found that functional connectivity between ventral temporal and the primary visual regions selectively increased during the processing of task-relevant information. Further, additional task demands selectively strengthen these targeted connectivity patterns. To identify candidate regions that contribute to this increase in inter-regional coupling, we regressed the task-specific time-varying connectivity strength between primary visual and occipitotemporal regions against voxel-wise activity patterns elsewhere in the brain. This allowed us to identify a set of frontal and parietal regions whose activity increased as a function of task-evoked functional connectivity. These results suggest that frontoparietal regions may provide top-down biasing signals to influence task-specific interactions between brain regions.
Exploring the economic viability of a mesopelagic fishery in the Bay of Biscay
Authors: Prellezo Raúl 
Published: January 2018

Abstract
The study analyses the economic viability of the mesopelagic fish exploitation. Operating characteristics of the selected bottom-trawl fleet operating in the Bay of Biscay were analysed on a trip basis, from the technical, financial and market perspectives. The results show that, while this activity is technically possible, it cannot be considered a viable financial alternative to the existing commercial fisheries. However, the landing obligation of the European Union Common Fisheries Policy, to become fully operational in 2019, provides an economic incentive in the form of alternative trips. The fishing effort is to be limited by this regulation. Thus, the discouraging opportunity costs of fishing mesopelagic species might be alleviated by the effort limitation. Additionally, the existing markets might expand, and new opportunities for commercial fisheries of mesopelagic species might be created. The sustainability of exploitation and its impact on the ecosystem services associated with these species should be considered in their management.