bluuebunny/crossref_metadata_2025_split huggingface dataset:
FAIM-L regulation of XIAP degradation modulates Synaptic Long-Term Depression and Axon Degeneration
Authors: Martínez-Mármol Ramón , Barneda-Zahonero Bruna , Soto David , Andrés Rosa Maria , Coccia Elena , Gasull Xavier , Planells-Ferrer Laura , Moubarak Rana S. , Soriano Eduardo , Comella Joan X. 
Published: October 2016

AbstractCaspases have recently emerged as key regulators of axonal pruning and degeneration and of long-term depression (LTD), a long-lasting form of synaptic plasticity. However, the mechanism underlying these functions remains unclear. In this context, XIAP has been shown to modulate these processes. The neuron-specific form of FAIM protein (FAIM-L) is a death receptor antagonist that stabilizes XIAP protein levels, thus preventing death receptor-induced neuronal apoptosis. Here we show that FAIM-L modulates synaptic transmission, prevents chemical-LTD induction in hippocampal neurons, and thwarts axon degeneration after nerve growth factor (NGF) withdrawal. Additionally, we demonstrate that the participation of FAIM-L in these two processes is dependent on its capacity to stabilize XIAP protein levels. Our data reveal FAIM-L as a regulator of axonal degeneration and synaptic plasticity.
The first oviraptorosaur (Dinosauria: Theropoda) bonebed: evidence of gregarious behaviour in a maniraptoran theropod
Authors: Funston Gregory F. , Currie Philip J. , Eberth David A. , Ryan Michael J. , Chinzorig Tsogtbaatar , Badamgarav Demchig , Longrich Nicholas R. 
Published: October 2016

AbstractA monodominant bonebed ofAvimimusfrom the Nemegt Formation of Mongolia is the first oviraptorosaur bonebed described and the only recorded maniraptoran bonebed from the Late Cretaceous. Cranial elements recovered from the bonebed provide insights on the anatomy of the facial region, which was formerly unknown inAvimimus. Both adult and subadult material was recovered from the bonebed, but small juveniles are underrepresented. The taphonomic and sedimentological evidence suggests that theAvimimusbonebed represents a perimortem gregarious assemblage. The near absence of juveniles in the bonebed may be evidence of a transient age-segregated herd or ‘flock’, but the behaviour responsible for this assemblage is unclear. Regardless, theAvimimusbonebed is the first evidence of gregarious behaviour in oviraptorosaurs, and highlights a potential trend of increasing gregariousness in dinosaurs towards the end of the Mesozoic.
The 2014 Ebola virus outbreak in West Africa highlights no evidence of rapid evolution or adaptation to humans
Authors: Li Xingguang , Zai Junjie , Liu Haizhou , Feng Yi , Li Fan , Wei Jing , Zou Sen , Yuan Zhiming , Shao Yiming 
Published: October 2016

AbstractFollowing its immergence in December 2013, the recent Zaire Ebola virus (EBOV) outbreak in West Africa has spread and persisted for more than two years, making it the largest EBOV epidemic in both scale and geographical region to date. In this study, a total of 726 glycoprotein (GP) gene sequences of the EBOV full-length genome obtained from West Africa from the 2014 outbreak, combined with 30 from earlier outbreaks between 1976 and 2008 were used to investigate the genetic divergence, evolutionary history, population dynamics, and selection pressure of EBOV among distinct epidemic waves. Results from our dataset showed that no non-synonymous substitutions occurred on the GP gene coding sequences of EBOV that were likely to have affected protein structure or function in any way. Furthermore, the significantly different dN/dS ratios observed between the 2014 West African outbreak and earlier outbreaks were more likely due to the confounding presence of segregating polymorphisms. Our results highlight no robust evidence that the 2014 EBOV outbreak is fast-evolving and adapting to humans. Therefore, the unprecedented nature of the 2014 EBOV outbreak might be more likely related to non-virological elements, such as environmental and sociological factors.
Amorphous titanium-oxide supercapacitors
Authors: Fukuhara Mikio , Kuroda Tomoyuki , Hasegawa Fumihiko 
Published: October 2016

AbstractThe electric capacitance of an amorphous TiO2-x surface increases proportionally to the negative sixth power of the convex diameter d. This occurs because of the van der Waals attraction on the amorphous surface of up to 7 mF/cm2, accompanied by extreme enhanced electron trapping resulting from both the quantum-size effect and an offset effect from positive charges at oxygen-vacancy sites. Here we show that a supercapacitor, constructed with a distributed constant-equipment circuit of large resistance and small capacitance on the amorphous TiO2-x surface, illuminated a red LED for 37 ms after it was charged with 1 mA at 10 V. The fabricated device showed no dielectric breakdown up to 1,100 V. Based on this approach, further advances in the development of amorphous titanium-dioxide supercapacitors might be attained by integrating oxide ribbons with a micro-electro mechanical system.
Oxidative stress dependent microRNA-34a activation via PI3Kα reduces the expression of sirtuin-1 and sirtuin-6 in epithelial cells
Authors: Baker J. R. , Vuppusetty C. , Colley T. , Papaioannou Andriana I. , Fenwick P. , Donnelly Louise , Ito K. , Barnes P. J. 
Published: October 2016

AbstractSirtuin-1 (SIRT1) and SIRT6, NAD+-dependent Class III protein deacetylases, are putative anti-aging enzymes, down-regulated in patients with chronic obstructive pulmonary disease (COPD), which is characterized by the accelerated ageing of the lung and associated with increased oxidative stress. Here, we show that oxidative stress (hydrogen peroxide) selectively elevates microRNA-34a (miR-34a) but not the related miR-34b/c, with concomitant reduction of SIRT1/-6 in bronchial epithelial cells (BEAS2B), which was also observed in peripheral lung samples from patients with COPD. Over-expression of a miR-34a mimic caused a significant reduction in both mRNA and protein of SIRT1/-6, whereas inhibition of miR-34a (antagomir) increased these sirtuins. Induction of miR-34a expression with H2O2 was phosphoinositide-3-kinase (PI3K) dependent as it was associated with PI3Kα activation as well as phosphatase and tensin homolog (PTEN) reduction. Importantly, miR-34a antagomirs increased SIRT1/-6 mRNA levels, whilst decreasing markers of cellular senescence in airway epithelial cells from COPD patients, suggesting that this process is reversible. Other sirtuin isoforms were not affected by miR-34a. Our data indicate that miR-34a is induced by oxidative stress via PI3K signaling, and orchestrates ageing responses under oxidative stress, therefore highlighting miR-34a as a new therapeutic target and biomarker in COPD and other oxidative stress-driven aging diseases.
Efficient recellularisation of decellularised whole-liver grafts using biliary tree and foetal hepatocytes
Authors: Ogiso Satoshi , Yasuchika Kentaro , Fukumitsu Ken , Ishii Takamichi , Kojima Hidenobu , Miyauchi Yuya , Yamaoka Ryoya , Komori Junji , Katayama Hokahiro , Kawai Takayuki , Yoshitoshi Elena Yukie , Kita Sadahiko , Yasuda Katsutaro , Uemoto Shinji 
Published: October 2016

AbstractA whole-organ regeneration approach, using a decellularised xenogeneic liver as a scaffold for the construction of a transplantable liver was recently reported. Deriving suitable scaffolds was the first step towards clinical application; however, effective recellularisation remains to be achieved. This report presents a strategy for the improvement of the recellularisation process, using novel cell-seeding technique and cell source. We evaluated recellularised liver grafts repopulated through the portal vein or the biliary duct with mice adult hepatocytes or E14.5 foetal hepatocytes. More than 80% of the cells seeded through the biliary tree entered the parenchyma beyond the ductule-lining matrix barrier and distributed throughout the liver lobule. In contrast, about 20% of the cells seeded through the portal tree entered the parenchyma. The gene expression levels of foetal hepatocyte albumin, glucose 6-phosphatase, transferrin, cytokeratin 19, and gamma-glutamyl transpeptidase were increased in three-dimensional cultures in the native liver-derived scaffolds, and the activation of liver detoxification enzymes and formation of biliary duct-like structures were supported. The metabolic functions of liver grafts recellularised with different cell types were similar. These results suggest that biliary tree cell-seeding approach is promising, and that liver progenitor cells represent a good cell source candidate.
Genomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing
Authors: Li Gang , Shen Mengyu , Le Shuai , Tan Yinling , Li Ming , Zhao Xia , Shen Wei , Yang Yuhui , Wang Jing , Zhu Hongbin , Li Shu , Rao Xiancai , Hu Fuquan , Lu Shuguang 
Published: October 2016

As a third-generation sequencing (TGS) method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for resequencing projects and de novo assembly. In the present study, Pseudomonas aeruginosa PA1 was characterized and resequenced using SMRT technology. PA1 was also subjected to genomic, comparative and pan-genomic analyses. The multidrug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins (RPs), secretion system proteins, type II toxin–antitoxin (T–A) pairs and genomic islands. Whole genome comparison analysis suggested that PA1 exhibits similarity to other P. aeruginosa strains but differs in terms of horizontal gene transfer (HGT) regions, such as prophages and genomic islands. Phylogenetic analyses based on 16S rRNA sequences demonstrated that PA1 is closely related to PAO1, and P. aeruginosa strains can be divided into two main groups. The pan-genome of P. aeruginosa consists of a core genome of approximately 4,000 genes and an accessory genome of at least 6,600 genes. The present study presented a detailed, visualized and comparative analysis of the PA1 genome, to enhance our understanding of this notorious pathogen.
Superoleophobic surfaces on stainless steel substrates obtained by chemical bath deposition
Authors: Huang Liu , Song Jinlong , Lu Yao , Chen Faze , Liu Xin , Jin Zhuji , Zhao Danyang , Carmalt Claire J. , Parkin Ivan P. 
Published: October 2016

Superhydrophobic surfaces have shown great potential in domestic and industrial applications. However, these surfaces lose their superhydrophobic functions once being contaminated by oily liquids. In this work a simple chemical bath deposition method is reported to fabricate superoleophobic surfaces on steel substrates that repel both water and oil. The synthesis of superoleophobic surfaces involves the fabrication of the micro/nanometre‐scale origami‐ball‐like structures on steel substrates, followed by the modification of low surface energy material. The fabricated surfaces have glycerol, peanut oil and hexadecane contact angles larger than 150° and roll‐off angles smaller than 10°. This method is highly efficient because it takes only 5 min to create the surface re‐entrant structures that are required by superoleophobicity. The prepared surfaces showed remarkable durability and retained superoleophobicity even after exposure to high and low temperatures (−30 and 100°C), and UV irradiation. This work will enrich the processing methods of the superoleophobic surfaces on stainless steel substrates.
Laminin targeting of a peripheral nerve-highlighting peptide enables degenerated nerve visualization
Authors: Glasgow Heather L. , Whitney Michael A. , Gross Larry A. , Friedman Beth , Adams Stephen R. , Crisp Jessica L. , Hussain Timon , Frei Andreas P. , Novy Karel , Wollscheid Bernd , Nguyen Quyen T. , Tsien Roger Y. 
Published: October 2016

Significance
A fluorescently labeled nerve-binding peptide, NP41, holds promise to reduce surgical nerve damage and facilitate nerve repair. Clinical translation hinges on identification of binding targets to assess potential toxicity and understand the mechanism. For target identification, we developed a receptor capture method, enabling covalent tagging and identification of proteins within close proximity to a bound ligand. Extracellular matrix proteins laminin-421 and -211 were identified as NP41 binding targets, and TRICEPS-based glycoprotein capture supported laminin-421 as the primary binding target. This result explains the ability of NP41 to highlight degenerated nerve “ghosts” months after transection that were invisible to the unaided eye but contain laminins. Targeting extracellular matrix is advantageous for clinical imaging agents, likely reducing undesirable neurological effects.
Commensurate 4
a
0
-period charge density modulations throughout the Bi
2
Sr
2
CaCu
2
O
8+x
pseudogap regime
Authors: Mesaros Andrej , Fujita Kazuhiro , Edkins Stephen D. , Hamidian Mohammad H. , Eisaki Hiroshi , Uchida Shin-ichi , Davis J. C. Séamus , Lawler Michael J. , Kim Eun-Ah 
Published: October 2016

Significance
Strong Coulomb interactions between electrons on adjacent Cu atoms result in charge localization in the cuprate Mott-insulator state. When a few percent of electrons are removed, both high-temperature superconductivity and exotic charge density modulations appear. Identifying the correct fundamental theory for superconductivity requires confidence on whether a particle-like or a wave-like concept of electrons describes this physics. To address this issue, here we take the approach of using the phase of charge modulations, available only from atomic-scale imaging. It reveals a universal periodicity of the charge modulations of four crystal unit cells. These results indicate that the particle-like concept of strong interactions in real-space provides the intrinsic organizational principle for cuprate charge modulations, implying the equivalent for the superconductivity.
Testing for Specification Bias with a Flexible Fourier Transform Model for Crop Yields
Authors: Cooper Joseph , Tran A. Nam , Wallander Steven 
Published: October 2016

AbstractThe literature on climate risk and crop yields is currently focused on the potential for highly non‐linear marginal effects, essentially modeling the threshold effects with a yield function that maps weather inputs into crop yields. Implicit in this line of research is the assertion that the traditional quadratic model of crop yield suffers from specification bias. This article examines this assumption by using the Flexible Fourier Transforms (FFT) to allow for global flexibility in the weather effects while also maintaining the traditional quadratic model as a nested model specification. In order to speak to the global flexibility of FFT, as well as to provide both robustness to outliers and information on the scale effects of weather variables, this article compares FFT with restricted cubic spline (RCS) and quadratic models in a quantile regression framework. Using U.S. county‐level data on corn, soybeans, and winter wheat from 1975 to 2013, we find that while the threshold effects are largely captured by the traditional quadratic model, we statistically reject the hypothesis that the quadratic model is sufficiently flexible. We find that, under the more flexible FFT functional forms, at lower temperatures there is a greater positive impact of marginal increases in temperature on yield than with the quadratic model, which suggests a different yield‐temperature relationship than found in much of the literature on threshold effects of temperature on crop yields, and is more consistent with the positive effects of minor temperature increases found in some of the Ricardian climate effect literature.
Listing and Delisting Thresholds under the Endangered Species Act
Authors: Sims Charles , Finnoff David , Hastings Alan , Hochard Jacob 
Published: October 2016

AbstractWe consider the case where a species provides a flow of economic benefits, is at risk of extinction, and is being considered for addition to the Endangered Species List. Listing a species as endangered is costly but increases the flow of social benefits and reduces the likelihood of extinction. If the species recovers sufficiently, additional costs can be incurred to subsequently delist the species. By treating listing and delisting as a pair of linked investment options, we provide an alternative to current practice for listing and delisting decisions that maximizes the return from public conservation investments. Under this alternative framework, we show that economic considerations may actually afford greater protection for at‐risk species if these decisions are initiated early. However, biological sources of uncertainty may cause those species most in need of protection to be passed over in favor of more stable species that represent a “sure bet” for species preservation.
The Number of Chandelier and Basket Cells Are Differentially Decreased in Prefrontal Cortex in Autism
Authors: Ariza Jeanelle , Rogers Haille , Hashemi Ezzat , Noctor Stephen C , Martínez-Cerdeño Verónica 
Published: October 2016

AbstractAn interneuron alteration has been proposed as a source for the modified balance of excitation / inhibition in the cerebral cortex in autism. We previously demonstrated a decreased number of parvalbumin (PV)-expressing interneurons in prefrontal cortex in autism. PV-expressing interneurons include chandelier (Ch) and basket (Bsk) cells. We asked whether the decreased PV+ interneurons affected both Ch cells and Bsk cells in autism. The lack of single markers to specifically label Ch cells or Bsk cells presented an obstacle for addressing this question. We devised a method to discern between PV-Ch and PV-Bsk cells based on the differential expression of Vicia villosa lectin (VVA). VVA binds to N-acetylgalactosamine, that is present in the perineuronal net surrounding some cell types where it plays a role in intercellular communication. N-acetylgalactosamine is present in the perineuronal net surrounding Bsk but not Ch cells. We found that the number of Ch cells is consistently decreased in the prefrontal cortex of autistic (n = 10) when compared with control (n = 10) cases, while the number of Bsk cells is not as severely affected. This finding expand our understanding of GABAergic system functioning in the human cerebral cortex in autism, which will impact translational research directed towards providing better treatment paradigms for individuals with autism.
Little evidence for entropy and energy excess beyond r500 - An end to ICM preheating?
Authors: Iqbal Asif , Majumdar Subhabrata , Nath Biman B. , Ettori Stefano , Eckert Dominique , Malik Manzoor A. 
Published: October 2016

Abstract
Non-gravitational feedback affects the nature of the intra-cluster medium (ICM). X-ray cooling of the ICM and in situ energy feedback from AGN’s and SNe as well as preheating of the gas at epochs preceding the formation of clusters are proposed mechanisms for such feedback. While cooling and AGN feedbacks are dominant in cluster cores, the signatures of a preheated ICM are expected to be present even at large radii. To estimate the degree of preheating, with minimum confusion from AGN feedback/cooling, we study the excess entropy and non-gravitational energy profiles upto r200 for a sample of 17 galaxy clusters using joint data sets of Planck SZ pressure and ROSAT/PSPC gas density profiles. The canonical value of preheating entropy floor of ≳ 300 keV cm2, needed in order to match cluster scalings, is ruled out at ≈3σ. We also show that the feedback energy of 1 keV/particle is ruled out at 5.2σ beyond r500. Our analysis takes both non-thermal pressure and clumping into account which can be important in outer regions. Our results based on the direct probe of the ICM in the outermost regions do not support any significant preheating.
Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
Authors: Ahlgren Nathan A , Ren Jie , Lu Yang Young , Fuhrman Jed A , Sun Fengzhu 
Published: October 2016

AbstractViruses and their host genomes often share similar oligonucleotide frequency (ONF) patterns, which can be used to predict the host of a given virus by finding the host with the greatest ONF similarity. We comprehensively compared 11 ONF metrics using several k-mer lengths for predicting host taxonomy from among ∼32 000 prokaryotic genomes for 1427 virus isolate genomes whose true hosts are known. The background-subtracting measure $d_2^*$ at k = 6 gave the highest host prediction accuracy (33%, genus level) with reasonable computational times. Requiring a maximum dissimilarity score for making predictions (thresholding) and taking the consensus of the 30 most similar hosts further improved accuracy. Using a previous dataset of 820 bacteriophage and 2699 bacterial genomes, $d_2^*$ host prediction accuracies with thresholding and consensus methods (genus-level: 64%) exceeded previous Euclidian distance ONF (32%) or homology-based (22-62%) methods. When applied to metagenomically-assembled marine SUP05 viruses and the human gut virus crAssphage, $d_2^*$-based predictions overlapped (i.e. some same, some different) with the previously inferred hosts of these viruses. The extent of overlap improved when only using host genomes or metagenomic contigs from the same habitat or samples as the query viruses. The $d_2^*$ ONF method will greatly improve the characterization of novel, metagenomic viruses.
East Asian observations of low-latitude aurora during the Carrington magnetic storm
Authors: Hayakawa Hisashi , Iwahashi Kiyomi , Tamazawa Harufumi , Isobe Hiroaki , Kataoka Ryuho , Ebihara Yusuke , Miyahara Hiroko , Kawamura Akito Davis , Shibata Kazunari 
Published: October 2016

Abstract
A magnetic storm around 1859 September 2, caused by a so-called Carrington flare, was the most intense in the history of modern scientific observations, and hence is considered to be a benchmark event concerning space weather. The magnetic storm caused worldwide observations of auroras, even at very low latitudes, such as Hawaii, Panama, or Santiago. Available magnetic-field measurements at Bombay, India, showed two peaks: the main was the Carrington event, which occurred in day time in East Asia; a second storm after the Carrington event occurred at night in East Asia. In this paper, we present results from surveys of aurora records in East Asia, which provide new information concerning the aurora activity of this important event. We found some new East Asian records of low-latitude aurora observations caused by a storm which occurred after the Carrington event. The size of the aurora belt of the second peak of the Carrington magnetic storm was even wider than that of usual low-latitude aurora events.
Extraocular Sebaceous Carcinoma—A Clinicopathologic Reassessment
Authors: Candelario Nicole M. , Sánchez Julio E. , Sánchez Jorge L. , Martín-García Rafael F. , Rochet Nicole M. 
Published: October 2016

Abstract:Sebaceous carcinoma is an aggressive adnexal neoplasm with sebaceous differentiation. Few reports have described the histopathologic characteristics of the sebaceous carcinoma occurring extraocularly. Seventy-two cases of extraocular sebaceous carcinoma were identified from the database of a Dermatopathology Laboratory from January 1, 2007 to May 31, 2013. More cases occurred in men (60%), with a mean age at diagnosis of 65.8 years (range 39–99 years). Neoplasms were histopathologically classified as well-differentiated (22%), moderately differentiated (67%), and poorly differentiated (11%). Sixty-seven percent (67%) of cases demonstrated a squamoid growth pattern and thirty-three percent (33%) demonstrated a basaloid growth pattern. A majority of the neoplasms histopathologically classified as well-differentiated (94%) and moderately differentiated (65%) demonstrated a squamoid growth pattern. Ten percent (10%) of cases exhibited cystic histopathologic changes. The histopathological features reported in this study aid in the understanding of extraocular sebaceous carcinoma and its eventual diagnosis and classification.