bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analyses across cattle genders and breeds reveal the pitfalls caused by false positive and lineage-differential copy number variations
Authors: Zhou Yang , Utsunomiya Yuri T. , Xu Lingyang , Hay El Hamidi abdel , Bickhart Derek M. , Sonstegard Tad S. , Van Tassell Curtis P. , Garcia Jose Fernando , Liu George E. 
Published: July 2016

AbstractWe compared CNV region (CNVR) results derived from 1,682 Nellore cattle with equivalent results derived from our previous analysis of Bovine HapMap samples. By comparing CNV segment frequencies between different genders and groups, we identified 9 frequent, false positive CNVRs with a total length of 0.8 Mbp that were likely caused by assembly errors. Although there was a paucity of lineage specific events, we did find one 54 kb deletion on chr5 significantly enriched in Nellore cattle. A few highly frequent CNVRs present in both datasets were detected within genomic regions containing olfactory receptor, ATP-binding cassette, and major histocompatibility complex genes. We further evaluated their impacts on downstream bioinformatics and CNV association analyses. Our results revealed pitfalls caused by false positive and lineage-differential copy number variations and will increase the accuracy of future CNV studies in both taurine and indicine cattle.
Patterns of theta oscillation reflect the neural basis of individual differences in epistemic motivation
Authors: Mussel Patrick , Ulrich Natalie , Allen John J. B. , Osinsky Roman , Hewig Johannes 
Published: July 2016

AbstractTheta oscillations in the EEG have been shown to reflect ongoing cognitive processes related to mental effort. Here, we show that the pattern of theta oscillation in response to varying cognitive demands reflects stable individual differences in the personality trait epistemic motivation: Individuals with high levels of epistemic motivation recruit relatively more cognitive resources in response to situations possessing high, compared to low, cognitive demand; individuals with low levels do not show such a specific response. Our results provide direct evidence for the theory of the construct need for cognition and add to our understanding of the neural processes underlying theta oscillations. More generally, we provide an explanation how individual differences in personality traits might be represented on a neural level.
Suppressing disease spreading by using information diffusion on multiplex networks
Authors: Wang Wei , Liu Quan-Hui , Cai Shi-Min , Tang Ming , Braunstein Lidia A. , Stanley H. Eugene 
Published: July 2016

AbstractAlthough there is always an interplay between the dynamics of information diffusion and disease spreading, the empirical research on the systemic coevolution mechanisms connecting these two spreading dynamics is still lacking. Here we investigate the coevolution mechanisms and dynamics between information and disease spreading by utilizing real data and a proposed spreading model on multiplex network. Our empirical analysis finds asymmetrical interactions between the information and disease spreading dynamics. Our results obtained from both the theoretical framework and extensive stochastic numerical simulations suggest that an information outbreak can be triggered in a communication network by its own spreading dynamics or by a disease outbreak on a contact network, but that the disease threshold is not affected by information spreading. Our key finding is that there is an optimal information transmission rate that markedly suppresses the disease spreading. We find that the time evolution of the dynamics in the proposed model qualitatively agrees with the real-world spreading processes at the optimal information transmission rate.
Serological detection of ‘Candidatus Liberibacter asiaticus’ in citrus, and identification by GeLC-MS/MS of a chaperone protein responding to cellular pathogens
Authors: Ding Fang , Duan Yongping , Yuan Qing , Shao Jonathan , Hartung John S. 
Published: July 2016

AbstractWe describe experiments with antibodies against ‘Candidatus Liberibacter asiaticus used to detect the pathogen in infected plants. We used scFv selected to bind epitopes exposed on the surface of the bacterium in tissue prints, with secondary monoclonal antibodies directed at a FLAG epitope included at the carboxyl end of the scFv. Unexpectedly, the anti-FLAG secondary antibody produced positive results with CaLas diseased samples when the primary scFv were not used. The anti-FLAG monoclonal antibody (Mab) also identified plants infected with other vascular pathogens. We then identified a paralogous group of secreted chaperone proteins in the HSP-90 family that contained the amino acid sequence DDDDK identical to the carboxy-terminal sequence of the FLAG epitope. A rabbit polyclonal antibody against one of the same epitopes combined with a goat anti-rabbit secondary antibody produced very strong purple color in individual phloem cells, as expected for this pathogen. These results were entirely specific for CaLas-infected citrus. The simplicity, cost and ability to scale the tissue print assay makes this an attractive assay to complement PCR-based assays currently in use. The partial FLAG epitope may itself be useful as a molecular marker for the rapid screening of citrus plants for the presence of vascular pathogens.
Mutations in the G-domain of Ski7 cause specific dysfunction in non-stop decay
Authors: Horikawa Wataru , Endo Kei , Wada Miki , Ito Koichi 
Published: July 2016

AbstractSki7 functions as a cofactor in both normal mRNA turnover and non-stop mRNA decay (NSD) mRNA surveillance in budding yeast. The N-terminal region of Ski7 (Ski7N) interacts with the ski-complex and the exosome. The C-terminal region of Ski7 (Ski7C) binds guanine nucleotides and shares overall sequence and structural homology with the proteins of the translational GTPase superfamily, especially the tRNA/tRNA-mimic carrier protein subfamilies such as EF1α, eRF3 and Hbs1. Previous reports showed that Ski7N polypeptide functions adequately in vivo, while Ski7C, if any, only slightly. Furthermore, Ski7C does not exhibit GTP-hydrolysing activities under normal conditions. Therefore, the physiological and functional significance of the conserved Ski7C is unclear. Here, we report strong genetic evidence suggesting differential roles for Ski7N and Ski7C in normal and specific mRNA turnover pathways by creating/isolating mutations in both Ski7N and Ski7C conserved motifs using indicator yeast strains. We concluded that Ski7C participates in mRNA surveillance as a regulatory module competitively with the Hbs1/Dom34 complex. Our results provide insights into the molecular regulatory mechanisms underlying mRNA surveillance.
Recipe for High Moment Materials with Rare-earth and 3d Transition Metal Composites
Authors: Autieri Carmine , Kumar P. Anil , Walecki Dirk , Webers Samira , Gubbins Mark A. , Wende Heiko , Sanyal Biplab 
Published: July 2016

AbstractMaterials with high volume magnetization are perpetually needed for the generation of sufficiently large magnetic fields by writer pole of magnetic hard disks, especially for achieving increased areal density in storage media. In search of suitable materials combinations for this purpose, we have employed density functional theory to predict the magnetic coupling between iron and gadolinium layers separated by one to several monolayers of 3d transition metals (Sc-Zn). We demonstrate that it is possible to find ferromagnetic coupling for many of them and in particular for the early transition metals giving rise to high moment. Cr and Mn are the only elements able to produce a significant ferromagnetic coupling for thicker spacer layers. We also present experimental results on two trilayer systems Fe/Sc/Gd and Fe/Mn/Gd. From the experiments, we confirm a ferromagnetic coupling between Fe and Gd across a 3 monolayers Sc spacer or a Mn spacer thicker than 1 monolayer. In addition, we observe a peculiar dependence of Fe/Gd magnetic coupling on the Mn spacer thickness.
The Effect of Crystal Face of Fe2O3 on the Electrochemical Performance for Lithium-ion Batteries
Authors: Chen Minmin , Zhao Enyue , Yan Qingbo , Hu Zhongbo , Xiao Xiaoling , Chen Dongfeng 
Published: July 2016

AbstractFe2O3 nanorods exposing (001) and (010) plane as well as Fe2O3 nanosheets exposing (001) plane have been successfully synthesized. Fe2O3 nanosheets exhibit better cycle performance and rate capabilities than that of Fe2O3 nanorods. The discharge capacity of Fe2O3 nanosheets can stabilize at 865 mAh/g at the rate of 0.2 C (1C = 1000 mA/g) and 570 mAh/g at the rate of 1.2 C after 80 cycles, which increased by 90% and 79% compared with 456 mAh/g and 318 mAh/g of Fe2O3 nanorods. In comparison with (010) plane, the (001) plane of hematite possesses larger packing density of Fe3+ and O2−, which is responsible for the superior electrochemical performances of Fe2O3 nanosheets than that of Fe2O3 nanorods. In addition, potentiostatic intermittent titration (PITT) results show the diffusion coefficients of Li+ (DLi) of Fe2O3 nanosheets is higher than that of Fe2O3 nanorods. The higher diffusion coefficients of Li+ is favorable for the excellent lithium-storage capabilities and rate capability of Fe2O3 nanosheets. Inspired by our results, we can design and synthesize Fe2O3 or other electrodes with high performances according to their structure features in future.
Dipeptidyl Peptidase-4 Inhibitor Increases Vascular Leakage in Retina through VE-cadherin Phosphorylation
Authors: Lee Choon-Soo , Kim Yun Gi , Cho Hyun-Jai , Park Jonghanne , Jeong Heewon , Lee Sang-Eun , Lee Seung-Pyo , Kang Hyun-Jae , Kim Hyo-Soo 
Published: July 2016

AbstractThe inhibitors of CD26 (dipeptidyl peptidase-4; DPP4) have been widely prescribed to control glucose level in diabetic patients. DPP4-inhibitors, however, accumulate stromal cell-derived factor-1α (SDF-1α), a well-known inducer of vascular leakage and angiogenesis both of which are fundamental pathophysiology of diabetic retinopathy. The aim of this study was to investigate the effects of DPP4-inhibitors on vascular permeability and diabetic retinopathy. DPP4-inhibitor (diprotin A or sitagliptin) increased the phosphorylation of Src and vascular endothelial-cadherin (VE-cadherin) in human endothelial cells and disrupted endothelial cell-to-cell junctions, which were attenuated by CXCR4 (receptor of SDF-1α)-blocker or Src-inhibitor. Disruption of endothelial cell-to-cell junctions in the immuno-fluorescence images correlated with the actual leakage of the endothelial monolayer in the transwell endothelial permeability assay. In the Miles assay, vascular leakage was observed in the ears into which SDF-1α was injected, and this effect was aggravated by DPP4-inhibitor. In the model of retinopathy of prematurity, DPP4-inhibitor increased not only retinal vascularity but also leakage. Additionally, in the murine diabetic retinopathy model, DPP4-inhibitor increased the phosphorylation of Src and VE-cadherin and aggravated vascular leakage in the retinas. Collectively, DPP4-inhibitor induced vascular leakage by augmenting the SDF-1α/CXCR4/Src/VE-cadherin signaling pathway. These data highlight safety issues associated with the use of DPP4-inhibitors.
3D patterned stem cell differentiation using thermo-responsive methylcellulose hydrogel molds
Authors: Lee Wonjae , Park Jon 
Published: July 2016

AbstractTissue-specific patterned stem cell differentiation serves as the basis for the development, remodeling and regeneration of the multicellular structure of the native tissues. We herein proposed a cytocompatible 3D casting process to recapitulate this patterned stem cell differentiation for reconstructing multicellular tissues in vitro. We first reconstituted the 2D culture conditions for stem cell fate control within 3D hydrogel by incorporating the sets of the diffusible signal molecules delivered through drug-releasing microparticles. Then, utilizing thermo-responsivity of methylcellulose (MC), we developed a cytocompatible casting process to mold these hydrogels into specific 3D configurations, generating the targeted spatial gradients of diffusible signal molecules. The liquid phase of the MC solution was viscous enough to adopt the shapes of 3D impression patterns, while the gelated MC served as a reliable mold for patterning the hydrogel prepolymers. When these patterned hydrogels were integrated together, the stem cells in each hydrogel distinctly differentiated toward individually defined fates, resulting in the formation of the multicellular tissue structure bearing the very structural integrity and characteristics as seen in vascularized bones and osteochondral tissues.
K-Ras and cyclooxygenase-2 coactivation augments intraductal papillary mucinous neoplasm and Notch1 mimicking human pancreas lesions
Authors: Chiblak Sara , Steinbauer Brigitte , Pohl-Arnold Andrea , Kucher Dagmar , Abdollahi Amir , Schwager Christian , Höft Birgit , Esposito Irene , Müller-Decker Karin 
Published: July 2016

AbstractMutational activation of K-Ras is an initiating event of pancreatic ductal adenocarcinomas (PDAC) that may develop either from pancreatic intraepithelial neoplasia (PanIN) or intraductal papillary mucinous neoplasms (IPMN). Cyclooxygenase-2 (COX-2)-derived prostaglandin E2 (PGE2) is causally related to pancreatic carcinogenesis. Here, we deciphered the impact of COX-2, a key modulator of inflammation, in concert with active mutant K-RasG12D on tumor burden and gene expression signature using compound mutant mouse lines. Concomitant activation of COX-2 and K-RasG12D accelerated the progression of pancreatic intraepithelial lesions predominantly with a cystic papillary phenotype resembling human IPMN. Transcriptomes derived from laser capture microdissected preneoplastic lesions of single and compound mutants revealed a signature that was significantly enriched in Notch1 signaling components. In vitro, Notch1 signaling was COX-2-dependent. In line with these findings, human IPMN stratified into intestinal, gastric and pancreatobillary types displayed Notch1 immunosignals with high prevalence, especially in the gastric lesions. In conclusion, a yet unknown link between activated Ras, protumorigenic COX-2 and Notch1 in IPMN onset was unraveled.
Spherulization as a process for the exudation of chemical cues by the encrusting sponge C. crambe
Authors: Ternon Eva , Zarate Lina , Chenesseau Sandrine , Croué Julie , Dumollard Rémi , Suzuki Marcelino T. , Thomas Olivier P. 
Published: July 2016

AbstractEcological interactions in the marine environment are now recognized to be partly held by chemical cues produced by marine organisms. In particular, sponges are sessile animals thought to rely on the bioactive substances they synthesize to ensure their development and defense. However, the mechanisms leading the sponges to use their specialized metabolites as chemical cues remain unknown. Here we report the constant release of bioactive polycyclic guanidinic alkaloids by the Mediterranean sponge Crambe crambe into the dissolved and the particulate phases using a targeted metabolomics study. These compounds were proven to be stored into already described specialized (spherulous) sponge cells and dispersed into the water column after release through the sponge exhaling channels (oscula), leading to a chemical shield surrounding the sponge. Low concentrations of these compounds were demonstrated to have teratogenic effects on embryos of a common sea squirt (ascidian). This mechanism of action called spherulization may therefore contribute to the ecological success of encrusting sponges that need to extend their substrate cover to expand.
A crystal-clear zebrafish for in vivo imaging
Authors: Antinucci Paride , Hindges Robert 
Published: July 2016

AbstractThe larval zebrafish (Danio rerio) is an excellent vertebrate model for in vivo imaging of biological phenomena at subcellular, cellular and systems levels. However, the optical accessibility of highly pigmented tissues, like the eyes, is limited even in this animal model. Typical strategies to improve the transparency of zebrafish larvae require the use of either highly toxic chemical compounds (e.g. 1-phenyl-2-thiourea, PTU) or pigmentation mutant strains (e.g. casper mutant). To date none of these strategies produce normally behaving larvae that are transparent in both the body and the eyes. Here we present crystal, an optically clear zebrafish mutant obtained by combining different viable mutations affecting skin pigmentation. Compared to the previously described combinatorial mutant casper, the crystal mutant lacks pigmentation also in the retinal pigment epithelium, therefore enabling optical access to the eyes. Unlike PTU-treated animals, crystal larvae are able to perform visually guided behaviours, such as the optomotor response, as efficiently as wild type larvae. To validate the in vivo application of crystal larvae, we performed whole-brain light-sheet imaging and two-photon calcium imaging of neural activity in the retina. In conclusion, this novel combinatorial pigmentation mutant represents an ideal vertebrate tool for completely unobstructed structural and functional in vivo investigations of biological processes, particularly when imaging tissues inside or between the eyes.
Inflammation in low back pain may be detected from the peripheral blood: suggestions for biomarker
Authors: Li Yong , Liu Jun , Liu Zong-zhi , Duan Da-peng 
Published: July 2016

Biomarker for prediction of development of low back pain, and disease progression in chronic conditions are virtually non-existent. In the present study, we examined evidence of inflammation in the peripheral blood and demonstrated significant changes in neuroinflammation markers in subjects with chronic low back pain in comparison with control subjects. The present study was performed using peripheral blood from subjects with chronic low back pain and age-matched control subjects. Western blotting, real-time RT-PCR, cell culture and in vitro assays were incorporated to perform the current study. We obtained evidence that the balance between proinflammatory and anti-inflammatory cytokines is misaligned, with decrease in interleukin-10 (IL-10) expression and increase in interleukin-6 (IL-6) expression. Furthermore, we demonstrated increase in CD16 monocyte expression. Cells were cultured under differential conditions to generate M1/M2 macrophages. In the macrophages, opioid secretory capacity was shown to be diminished. Finally, Dragon (repulsive guidance molecule b, RGMb) expression was shown diminished in M1 macrophages, which serves as a key transcriptional inhibitor of IL-6 expression. These biochemical and cellular alterations in chronic low back pain can serve as potential biomarkers for assessing disease initiation, intensity and progression.
Quantifying the origins of life on a planetary scale
Authors: Scharf Caleb , Cronin Leroy 
Published: July 2016

Significance
In this paper, we describe an equation to estimate the frequency of planetary “origin of life”-type events that is similar in intent to the Drake Equation but with some key advantages—specifically, our formulation makes an explicit connection between “global” rates for life arising and granular information about a planet. Our approach indicates scenarios where a shared chemical search space with more complex building blocks could be the critical difference between cosmic environments where life is potentially more or less abundant but, more importantly, points to constraints on the search. The possibility of chemical search-space amplification could be a major variance factor in planetary abiogenesis probabilities.
pH-degradable imidazoquinoline-ligated nanogels for lymph node-focused immune activation
Authors: Nuhn Lutz , Vanparijs Nane , De Beuckelaer Ans , Lybaert Lien , Verstraete Glenn , Deswarte Kim , Lienenklaus Stefan , Shukla Nikunj M. , Salyer Alex C. D. , Lambrecht Bart N. , Grooten Johan , David Sunil A. , De Koker Stefaan , De Geest Bruno G. 
Published: July 2016

Significance
The newest generation of small-molecule vaccine adjuvants aims at triggering specific receptors expressed by dendritic cells, the working horses of our immune system. Unfortunately, owing to their small size, upon administration these molecules rapidly enter systemic circulation and cause systemic inflammation. We report on a nanotechnology-based solution for this issue by covalent ligation of a potent immunostimulatory small molecule to hydrogel nanoparticles. This approach allows for lymph node-restricted immune activation and avoids systemic dissemination. Importantly, relative to soluble immunostimulatory compound, nanoparticle ligation yields increased immune activation in the draining lymph nodes and results in strongly increased antibody titers and T-cell responses against an admixed vaccine antigen.
Blood sugar level follows perceived time rather than actual time in people with type 2 diabetes
Authors: Park Chanmo , Pagnini Francesco , Reece Andrew , Phillips Deborah , Langer Ellen 
Published: July 2016

Significance
We investigated the hypothesis that the perception of time passing can exert a stronger influence on blood glucose level compared with the passage of actual time in people with type 2 diabetes. Our findings suggest that manipulation of participants’ perception of time resulted in blood glucose levels changing in accordance with how much time participants believed had passed, instead of how much time had actually passed. These results are an important example of the influence psychological processes can directly exert on the body. Mindsets and expectations may play an increasingly important role in type 2 diabetes management.
Cook Island artifact geochemistry demonstrates spatial and temporal extent of pre-European interarchipelago voyaging in East Polynesia
Authors: Weisler Marshall I. , Bolhar Robert , Ma Jinlong , St Pierre Emma , Sheppard Peter , Walter Richard K. , Feng Yuexing , Zhao Jian-xin , Kirch Patrick V. 
Published: July 2016

SignificanceOceania, the last region settled on Earth, witnessed the greatest maritime migration in human history. Scholars have debated how and when islands were colonized and the role of postsettlement voyaging in maintaining founding colonies and in subsequent diversification of island societies. We geochemically “fingerprinted” exotic stone artifacts from a well-dated archaeological site in the Cook Islands, matching artifacts to their geological sources and demonstrating that the geographical voyaging network extended beyond the Cook Islands to include the Austral, Samoa, and Marquesas archipelagos—up to 2,400 km distant. We further demonstrate that Polynesian interarchipelago voyaging lasted from about AD 1300 to the 1600s, suggesting that long-distance interaction continued to influence the development of social structures in East Polynesia well after initial colonization.