bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global climate change driven by soot at the K-Pg boundary as the cause of the mass extinction
Authors: Kaiho Kunio , Oshima Naga , Adachi Kouji , Adachi Yukimasa , Mizukami Takuya , Fujibayashi Megumu , Saito Ryosuke 
Published: July 2016

AbstractThe mass extinction of life 66 million years ago at the Cretaceous/Paleogene boundary, marked by the extinctions of dinosaurs and shallow marine organisms, is important because it led to the macroevolution of mammals and appearance of humans. The current hypothesis for the extinction is that an asteroid impact in present-day Mexico formed condensed aerosols in the stratosphere, which caused the cessation of photosynthesis and global near-freezing conditions. Here, we show that the stratospheric aerosols did not induce darkness that resulted in milder cooling than previously thought. We propose a new hypothesis that latitude-dependent climate changes caused by massive stratospheric soot explain the known mortality and survival on land and in oceans at the Cretaceous/Paleogene boundary. The stratospheric soot was ejected from the oil-rich area by the asteroid impact and was spread globally. The soot aerosols caused sufficiently colder climates at mid–high latitudes and drought with milder cooling at low latitudes on land, in addition to causing limited cessation of photosynthesis in global oceans within a few months to two years after the impact, followed by surface-water cooling in global oceans in a few years. The rapid climate change induced terrestrial extinctions followed by marine extinctions over several years.
Carbon Storage Patterns of Caragana korshinskii in Areas of Reduced Environmental Moisture on the Loess Plateau, China
Authors: Gong Chunmei , Bai Juan , Wang Junhui , Zhou Yulu , Kang Tai , Wang Jiajia , Hu Congxia , Guo Hongbo , Chen Peilei , Xie Pei , Li Yuanfeng 
Published: July 2016

AbstractPrecipitation patterns are influenced by climate change and profoundly alter the carbon sequestration potential of ecosystems. Carbon uptake by shrubbery alone accounts for approximately one-third of the total carbon sink; however, whether such uptake is altered by reduced precipitation is unclear. In this study, five experimental sites characterised by gradual reductions in precipitation from south to north across the Loess Plateau were used to evaluate theCaragana korshinskii’s functional and physiological features, particularly its carbon fixation capacity, as well as the relationships among these features. We found the improved net CO2assimilation rates and inhibited transpiration at the north leaf were caused by lower canopy stomatal conductance, which enhanced the instantaneous water use efficiency and promoted plant biomass as well as carbon accumulation. Regional-scale precipitation reductions over a certain range triggered a distinct increase in the shrub’s organic carbon storage with an inevitable decrease in the soil’s organic carbon storage. Our results confirmC. korshinskiiis the optimal dominant species for the reconstruction of fragile dryland ecosystems. The patterns of organic carbon storage associated with this shrub occurred mostly in the soil at wetter sites, and in the branches and leaves at drier sites across the arid and semi-arid region.
Human Thanatomicrobiome Succession and Time Since Death
Authors: Javan Gulnaz T. , Finley Sheree J. , Can Ismail , Wilkinson Jeremy E. , Hanson J. Delton , Tarone Aaron M. 
Published: July 2016

AbstractThe thanatomicrobiome (thanatos, Greek for death) is a relatively new term and is the study of the microbes colonizing the internal organs and orifices after death. Recent scientific breakthroughs in an initial study of the thanatomicrobiome have revealed that a majority of the microbes within the human body are the obligate anaerobes,Clostridium spp., in the internal postmortem microbial communities. We hypothesized that time-dependent changes in the thanatomicrobiome within internal organs can estimate the time of death as a human body decays. Here we report a cross-sectional study of the sampling of 27 human corpses from criminal cases with postmortem intervals between 3.5–240 hours. The impetus for examining microbial communities in different internal organs is to address the paucity of empirical data on thanatomicrobiomic succession caused by the limited access to these organs prior to death and a dearth of knowledge regarding the movement of microbes within remains. Our sequencing results of 16S rRNA gene amplicons of 27 postmortem samples from cadavers demonstrated statistically significant time-, organ- and sex-dependent changes. These results suggest that comprehensive knowledge of the number and abundance of each organ’s signature microorganisms could be useful to forensic microbiologists as a new source of data for estimating postmortem interval.
Mediterranean circulation perturbations over the last five centuries: Relevance to past Eastern Mediterranean Transient-type events
Authors: Incarbona Alessandro , Martrat Belen , Mortyn P. Graham , Sprovieri Mario , Ziveri Patrizia , Gogou Alexandra , Jordà Gabriel , Xoplaki Elena , Luterbacher Juerg , Langone Leonardo , Marino Gianluca , Rodríguez-Sanz Laura , Triantaphyllou Maria , Di Stefano Enrico , Grimalt Joan O. , Tranchida Giorgio , Sprovieri Rodolfo , Mazzola Salvatore 
Published: July 2016

AbstractThe Eastern Mediterranean Transient (EMT) occurred in the Aegean Sea from 1988 to 1995 and is the most significant intermediate-to-deep Mediterranean overturning perturbation reported by instrumental records. The EMT was likely caused by accumulation of high salinity waters in the Levantine and enhanced heat loss in the Aegean Sea, coupled with surface water freshening in the Sicily Channel. It is still unknown whether similar transients occurred in the past and, if so, what their forcing processes were. In this study, sediments from the Sicily Channel document surface water freshening (SCFR) at 1910 ± 12, 1812 ± 18, 1725 ± 25 and 1580 ± 30 CE. A regional ocean hindcast links SCFR to enhanced deep-water production and in turn to strengthened Mediterranean thermohaline circulation. Independent evidence collected in the Aegean Sea supports this reconstruction, showing that enhanced bottom water ventilation in the Eastern Mediterranean was associated with each SCFR event. Comparison between the records and multi-decadal atmospheric circulation patterns and climatic external forcings indicates that Mediterranean circulation destabilisation occurs during positive North Atlantic Oscillation (NAO) and negative Atlantic Multidecadal Oscillation (AMO) phases, reduced solar activity and strong tropical volcanic eruptions. They may have recurrently produced favourable deep-water formation conditions, both increasing salinity and reducing temperature on multi-decadal time scales.
Annexin A1 contributes to pancreatic cancer cell phenotype, behaviour and metastatic potential independently of Formyl Peptide Receptor pathway
Authors: Belvedere Raffaella , Bizzarro Valentina , Forte Giovanni , Dal Piaz Fabrizio , Parente Luca , Petrella Antonello 
Published: July 2016

AbstractAnnexin A1 (ANXA1) is a Ca2+-binding protein over-expressed in pancreatic cancer (PC). We recently reported that extracellular ANXA1 mediates PC cell motility acting on Formyl Peptide Receptors (FPRs). Here, we describe other mechanisms by which intracellular ANXA1 could mediate PC progression. We obtained ANXA1 Knock-Out (KO) MIA PaCa-2 cells using the CRISPR/Cas9 genome editing technology. LC-MS/MS analysis showed altered expression of several proteins involved in cytoskeletal organization. As a result, ANXA1 KO MIA PaCa-2 partially lost their migratory and invasive capabilities with a mechanism that appeared independent of FPRs. The acquisition of a less aggressive phenotype has been further investigated in vivo. Wild type (WT), PGS (scrambled) and ANXA1 KO MIA PaCa-2 cells were engrafted orthotopically in SCID mice. No differences were found about PC primary mass, conversely liver metastatization appeared particularly reduced in ANXA1 KO MIA PaCa-2 engrafted mice. In summary, we show that intracellular ANXA1 is able to preserve the cytoskeleton integrity and to maintain a malignant phenotype in vitro. The protein has a relevant role in the metastatization process in vivo, as such it appears attractive and suitable as prognostic and therapeutic marker in PC progression.
ROCK1 reduces mitochondrial content and irisin production in muscle suppressing adipocyte browning and impairing insulin sensitivity
Authors: Zhou Xiaoshuang , Li Rongshan , Liu Xinyan , Wang Lihua , Hui Peng , Chan Lawrence , Saha Pradip K. , Hu Zhaoyong 
Published: July 2016

AbstractIrisin reportedly promotes the conversion of preadipocytes into “brown-like” adipocytes within subcutaneous white adipose tissue (WAT) via a mechanism that stimulates UCP-1 expression. An increase in plasma irisin has been associated with improved obesity and insulin resistance in mice with type 2 diabetes. But whether a low level of irisin stimulates the development of obesity has not been determined. In studying mice with muscle-specific constitutive ROCK1 activation (mCaROCK1), we found that irisin production was down-regulated and the mice developed obesity and insulin resistance. Therefore, we studied the effects of irisin deficiency on energy metabolism in mCaROCK1 mice. Constitutively activation of ROCK1 in muscle suppressed irisin expression in muscle resulting in a low level of irisin in circulation. Irisin deficiency reduced heat production and decreased the expression of uncoupling protein 1 (UCP1) in brown adipose tissue (BAT) and subcutaneous WAT. Moreover, mCaROCK1 mice also displayed impaired glucose tolerance. Notably, irisin replenishment in mCaROCK1 mice partially reversed insulin resistance and obesity and these changes were associated with increased expression of UCP1 and Pref-1 in subcutaneous WAT. These results demonstrate that irisin mediates muscle-adipose tissue communication and regulates energy and glucose homeostasis. Irisin administration can correct obesity and insulin resistance in mice.
The High Radiosensitizing Efficiency of a Trace of Gadolinium-Based Nanoparticles in Tumors
Authors: Dufort Sandrine , Le Duc Géraldine , Salomé Murielle , Bentivegna Valerie , Sancey Lucie , Bräuer-Krisch Elke , Requardt Herwig , Lux François , Coll Jean-Luc , Perriat Pascal , Roux Stéphane , Tillement Olivier 
Published: July 2016

AbstractWe recently developed the synthesis of ultrasmall gadolinium-based nanoparticles (GBN), (hydrodynamic diameter <5 nm) characterized by a safe behavior after intravenous injection (renal clearance, preferential accumulation in tumors). Owing to the presence of gadolinium ions, GBN can be used as contrast agents for magnetic resonance imaging (MRI) and as radiosensitizers. The attempt to determine the most opportune delay between the intravenous injection of GBN and the irradiation showed that a very low content of radiosensitizing nanoparticles in the tumor area is sufficient (0.1 μg/g of particles, i.e. 15 ppb of gadolinium) for an important increase of the therapeutic effect of irradiation. Such a promising and unexpected result is assigned to a suited distribution of GBN within the tumor, as revealed by the X-ray fluorescence (XRF) maps.
Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing
Authors: Shin Jongoh , Lee Sooin , Go Min-Jeong , Lee Sang Yup , Kim Sun Chang , Lee Chul-Ho , Cho Byung-Kwan 
Published: July 2016

AbstractDemands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-generation sequencing technologies have facilitated the elucidation of the microbial community composition with higher accuracy and greater throughput than was previously achievable; however, the short sequencing reads often limit the microbial composition analysis at the species level due to the high similarity of 16S rRNA amplicon sequences. To overcome this limitation, we used the nanopore sequencing platform to sequence full-length 16S rRNA amplicon libraries prepared from the mouse gut microbiota. A comparison of the nanopore and short-read sequencing data showed that there were no significant differences in major taxonomic units (89%) except one phylotype and three taxonomic units. Moreover, both sequencing data were highly similar at all taxonomic resolutions except the species level. At the species level, nanopore sequencing allowed identification of more species than short-read sequencing, facilitating the accurate classification of the bacterial community composition. Therefore, this method of full-length 16S rRNA amplicon sequencing will be useful for rapid, accurate and efficient detection of microbial diversity in various biological and clinical samples.
Roles of OA1 octopamine receptor and Dop1 dopamine receptor in mediating appetitive and aversive reinforcement revealed by RNAi studies
Authors: Awata Hiroko , Wakuda Ryo , Ishimaru Yoshiyasu , Matsuoka Yuji , Terao Kanta , Katata Satomi , Matsumoto Yukihisa , Hamanaka Yoshitaka , Noji Sumihare , Mito Taro , Mizunami Makoto 
Published: July 2016

AbstractRevealing reinforcing mechanisms in associative learning is important for elucidation of brain mechanisms of behavior. In mammals, dopamine neurons are thought to mediate both appetitive and aversive reinforcement signals. Studies using transgenic fruit-flies suggested that dopamine neurons mediate both appetitive and aversive reinforcements, through the Dop1 dopamine receptor, but our studies using octopamine and dopamine receptor antagonists and using Dop1 knockout crickets suggested that octopamine neurons mediate appetitive reinforcement and dopamine neurons mediate aversive reinforcement in associative learning in crickets. To fully resolve this issue, we examined the effects of silencing of expression of genes that code the OA1 octopamine receptor and Dop1 and Dop2 dopamine receptors by RNAi in crickets. OA1-silenced crickets exhibited impairment in appetitive learning with water but not in aversive learning with sodium chloride solution, while Dop1-silenced crickets exhibited impairment in aversive learning but not in appetitive learning. Dop2-silenced crickets showed normal scores in both appetitive learning and aversive learning. The results indicate that octopamine neurons mediate appetitive reinforcement via OA1 and that dopamine neurons mediate aversive reinforcement via Dop1 in crickets, providing decisive evidence that neurotransmitters and receptors that mediate appetitive reinforcement indeed differ among different species of insects.
Oncogenic KRAS triggers MAPK-dependent errors in mitosis and MYC-dependent sensitivity to anti-mitotic agents
Authors: Perera David , Venkitaraman Ashok R. 
Published: July 2016

AbstractOncogenic KRAS induces cell proliferation and transformation, but little is known about its effects on cell division. Functional genetic screens have recently revealed that cancer cell lines expressing oncogenic KRAS are sensitive to interference with mitosis, but neither the mechanism nor the uniformity of anti-mitotic drug sensitivity connected with mutant KRAS expression are yet clear. Here, we report that acute expression of oncogenic KRAS in HeLa cells induces mitotic delay and defects in chromosome segregation through mitogen-activated protein kinase (MAPK) pathway activation and de-regulated expression of several mitosis-related genes. These anomalies are accompanied by increased sensitivity to anti-mitotic agents, a phenotype dependent on the transcription factor MYC and its downstream target anti-apoptotic protein BCL-XL. Unexpectedly, we find no correlation between KRAS mutational status or MYC expression levels and anti-mitotic drug sensitivity when surveying a large database of anti-cancer drug responses. However, we report that the co-existence of KRAS mutations and high MYC expression predicts anti-mitotic drug sensitivity. Our findings reveal a novel function of oncogenic KRAS in regulating accurate mitotic progression and suggest new avenues to therapeutically target KRAS-mutant tumours and stratify patients in ongoing clinical trials of anti-mitotic drugs.
Highly Selective Enrichment of Glycopeptides Based on Zwitterionically Functionalized Soluble Nanopolymers
Authors: Cao Weiqian , Huang Jiangming , Jiang Biyun , Gao Xing , Yang Pengyuan 
Published: July 2016

AbstractEfficient glycopeptides enrichment prior to mass spectrometry analysis is essential for glycoproteome study. ZIC-HILIC (zwitterionic hydrophilic interaction liquid chromatography) based glycopeptides enrichment approaches have been attracting more attention for several benefits like easy operating, high enrichment specificity and intact glycopeptide retained. In this study, Poly (amidoamine) dendrimer (PAMAM) was adopted for the synthesis of zwitterionically functionalized (ZICF) materials for glycopeptide enrichment. The multiple branched structure and good solubility of ZICF-PAMAM enables a sufficient interaction with glycopeptides. The ZICF-PAMAM combined with the FASP-mode enrichment strategy exhibits more superior performance compared with the existing methods. It has the minimum detectable concentration of femtomolar level and high recovery rate of over 90.01%, and can efficiently enrich glycopeptides from complex biological samples even for merely 0.1 μL human serum. The remarkable glycopeptides enrichment capacity of ZICF-PAMAM highlights the potential application in in-depth glycoproteome research, which may open up new opportunities for the development of glycoproteomics.
An efficient method for gene silencing in human primary plasmacytoid dendritic cells: silencing of the TLR7/IRF-7 pathway as a proof of concept
Authors: Smith Nikaïa , Vidalain Pierre-Olivier , Nisole Sébastien , Herbeuval Jean-Philippe 
Published: July 2016

AbstractPlasmacytoid dendritic cells (pDC) are specialized immune cells that produce massive levels of type I interferon in response to pathogens. Unfortunately, pDC are fragile and extremely rare, rendering their functional study a tough challenge. However, because of their central role in numerous pathologies, there is a considerable need for an efficient and reproducible protocol for gene silencing in these cells. In this report, we tested six different methods for siRNA delivery into primary human pDC including viral-based, lipid-based, electroporation and poly-ethylenimine (PEI) technologies. We show that lipid-based reagent DOTAP was extremely efficient for siRNA delivery into pDC and did not induce cell death or pDC activation. We successfully silenced Toll-Like Receptor 7 (TLR7), CXCR4 and IFN regulatory factor 7 (IRF-7) gene expression in pDC as assessed by RT-qPCR or cytometry. Finally, we showed that TLR7 or IRF-7 silencing in pDC specifically suppressed IFN-α production upon stimulation, providing a functional validation of our transfection protocol.
Reliability of the Three-minute All-out Test for Non-motorized Treadmill Tethered Running
Authors: Gama M. , Sousa F.A. , dos Reis I.G. , Gobatto C. 
Published: July 2016

AbstractThe 3-min all-out test was developed and validated on a cycle ergometer using a modification of a linear mathematical equation (1/time vs. power) obtained from the original critical power model. The purpose of this development was to obtain, in a single test, the aerobic and anaerobic capacity parameters and identify the exercise transition moment from heavy to severe intensity. The aim of this study was to propose an adaptation of the all-out 3-min cycle ergometer to a non-motorized treadmill with tethered running. In addition, we tested the reproducibility of this adapted protocol, highlighting the need for mechanical power evaluation using a specific ergometer. Consequently, 10 physically active individuals visited the laboratory 4 times for testing and data collection. The results suggested that the protocol adaptation for the 3-min all-out test for non-motorized treadmill with tethered running was reproducible and feasible. It was also possible to show that the AO3 application in this ergometer ensures the specificity of the sports that involve the running exercise, from assessment of both aerobic and anaerobic parameters, accomplished in a single day of application.
Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates
Authors: Leung Kaston , Klaus Anders , Lin Bill K. , Laks Emma , Biele Justina , Lai Daniel , Bashashati Ali , Huang Yi-Fei , Aniba Radhouane , Moksa Michelle , Steif Adi , Mes-Masson Anne-Marie , Hirst Martin , Shah Sohrab P. , Aparicio Samuel , Hansen Carl L. 
Published: July 2016

Significance
The study of cell-to-cell genomic differences in complex multicellular systems such as cancer requires genome sequencing of large numbers of single cells. This in turn necessitates the uniform amplification of single-cell genomes with high reproducibility across large numbers of cells, which remains an outstanding challenge. Here, we introduce a method that uses commercially available liquid dispensing to perform inexpensive and high-throughput single-cell whole genome amplification (WGA) in nanoliter volumes. For the first time, to our knowledge, we demonstrate robust and highly uniform nanoliter-volume single-cell WGA across a large replicate set consisting of more than 100 single cells. Comparison with previous datasets shows that this method improves uniformity and achieves levels of genome coverage and genomic variant detection comparable or superior to existing methods.
Thermodynamic control of anvil cloud amount
Authors: Bony Sandrine , Stevens Bjorn , Coppin David , Becker Tobias , Reed Kevin A. , Voigt Aiko , Medeiros Brian 
Published: July 2016

Significance
Assessing the response of clouds to global warming remains a challenge of climate science. Past research has elucidated what controls the height and temperature of high-level anvil clouds, but the factors that control their horizontal extent remained uncertain. We show that the anvil cloud amount is expected to shrink as the climate warms or when convection becomes more clustered, due to a mechanism rooted in basic energetic and thermodynamic properties of the atmosphere. It is supported by three climate models and consistent with results from a cloud-resolving model and observations. We thus believe that this mechanism is robust and that it adds a new piece to understanding how clouds respond to climate warming.
Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds
Authors: Padhorny Dzmitry , Kazennov Andrey , Zerbe Brandon S. , Porter Kathryn A. , Xia Bing , Mottarella Scott E. , Kholodov Yaroslav , Ritchie David W. , Vajda Sandor , Kozakov Dima 
Published: July 2016

Significance
Expressing the interaction energy as sum of correlation functions, fast Fourier transform (FFT) based methods speed the calculation, enabling the sampling of billions of putative protein–protein complex conformations. However, such acceleration is currently achieved only on a 3D subspace of the full 6D rotational/translational space, and the remaining dimensions must be sampled using conventional slow calculations. Here we present an algorithm that employs FFT-based sampling on the 5D rotational space, and only the 1D translations are sampled conventionally. The accuracy of the results is the same as those of earlier methods, but the calculation is an order of magnitude faster. Also, it is inexpensive computationally to add more correlation function terms to the scoring function compared with classical approaches.