bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thank you to Earth's Future Reviewers in 2018
Authors: van der Pluijm Ben , AghaKouchak Amir , Brasseur Guy , Ellis Michael , Grimm Nancy , Liao Hong , Mari Céline H. , Romero‐Lankao Paty 
Published: June 2019

AbstractPeer review is one of the most important professional activities for scientists, because it ensures the quality of science that is shared with colleagues and with the world. Reviewers generously donate their time and effort with the knowledge that are key to sustaining scientific rigor. Earth's Future is fortunate to engage excellent reviewers that support the growth and reputation of our young journal as it receives and publishes high‐quality, high‐impact articles. We recognize the time, effort, and dedication that each review requires and extend a heartfelt thank you to all of our reviewers. Last year, Earth's Future received 395 peer reviews from 297 individuals that are listed below; reviewers who contributed three or more reviews are recognized in italics. Our acceptance rate remains steady at ~40%, while the number of submissions continue to increase at a healthy pace (269 in 2018).Thank you all for your important and valued contributions to our science in 2018.
Coupled Crust‐Mantle Response to Slab Tearing, Bending, and Rollback Along the Dinaride‐Hellenide Orogen
Authors: Handy Mark R. , Giese Joerg , Schmid Stefan M. , Pleuger Jan , Spakman Wim , Onuzi Kujtim , Ustaszewski Kamil 
Published: June 2019

AbstractWe integrate structural, geophysical, and geodetic studies showing that the Dinarides‐Hellenides orogen along the Adria‐Europe plate boundary in the Western Balkan peninsula has experienced clockwise oroclinal bending since Eocene‐Oligocene time. Rotation of the Hellenic segment of this orogen has accelerated since the middle Miocene and is associated with a north‐to‐south increase in shortening along the orogenic front. Within the Paleogene nappe pile, bending was accommodated by orogen‐parallel extension, clockwise block rotation, and thrusting in the hanging wall of the Skhoder‐Peja Normal Fault (SPNF). The SPNF and related faults cut the older Skhoder‐Peja Transfer Zone with its pre‐Neogene dextral offset of the West Vardar ophiolite nappe. Rotation of the SPNF hanging wall involved Miocene‐to‐recent, out‐of‐sequence thrusting that was transferred to the Hellenic orogenic front via lateral ramps on dextral transfer zones. Along strike of the Dinarides‐Hellenides and coincident with the southward increase in Neogene shortening, the depth of the Adriatic slab increases from ~160 km north of the SPNF to ~200 km just to the south thereof, to several hundreds of kilometers to the south of the Kefalonia Transfer Zone. The geodynamic driver of tectonics since the early Miocene has been enhanced rollback of the Hellenic segment of the Adriatic slab in the aftermath of Eocene‐Oligocene slab tearing and breakoff beneath the Dinarides, which focused slab pull in the south. The SW‐retreating Hellenic slab segment induced clockwise bending of the southern Dinarides and northern Hellenides, including their Adriatic foreland, about a rotation pole in the vicinity of the Mid‐Adriatic Ridge.
Isolation of intact bacteria from blood by selective cell lysis in a microfluidic porous silica monolith
Authors: Han Jung Y. , Wiederoder Michael , DeVoe Don L. 
Published: June 2019

AbstractRapid and efficient isolation of bacteria from complex biological matrices is necessary for effective pathogen identification in emerging single-cell diagnostics. Here, we demonstrate the isolation of intact and viable bacteria from whole blood through the selective lysis of blood cells during flow through a porous silica monolith. Efficient mechanical hemolysis is achieved while providing passage of intact and viable bacteria through the monoliths, allowing size-based isolation of bacteria to be performed following selective lysis. A process for synthesizing large quantities of discrete capillary-bound monolith elements and millimeter-scale monolith bricks is described, together with the seamless integration of individual monoliths into microfluidic chips. The impact of monolith morphology, geometry, and flow conditions on cell lysis is explored, and flow regimes are identified wherein robust selective blood cell lysis and intact bacteria passage are achieved for multiple gram-negative and gram-positive bacteria. The technique is shown to enable rapid sample preparation and bacteria analysis by single-cell Raman spectrometry. The selective lysis technique presents a unique sample preparation step supporting rapid and culture-free analysis of bacteria for the point of care.
Hepatic ferroptosis plays an important role as the trigger for initiating inflammation in nonalcoholic steatohepatitis
Authors: Tsurusaki Shinya , Tsuchiya Yuichi , Koumura Tomoko , Nakasone Misaki , Sakamoto Taro , Matsuoka Masaki , Imai Hirotaka , Yuet-Yin Kok Cindy , Okochi Hitoshi , Nakano Hiroyasu , Miyajima Atsushi , Tanaka Minoru 
Published: June 2019

AbstractNonalcoholic steatohepatitis (NASH) is a metabolic liver disease that progresses from simple steatosis to the disease state of inflammation and fibrosis. Previous studies suggest that apoptosis and necroptosis may contribute to the pathogenesis of NASH, based on several murine models. However, the mechanisms underlying the transition of simple steatosis to steatohepatitis remain unclear, because it is difficult to identify when and where such cell deaths begin to occur in the pathophysiological process of NASH. In the present study, our aim is to investigate which type of cell death plays a role as the trigger for initiating inflammation in fatty liver. By establishing a simple method of discriminating between apoptosis and necrosis in the liver, we found that necrosis occurred prior to apoptosis at the onset of steatohepatitis in the choline-deficient, ethionine-supplemented (CDE) diet model. To further investigate what type of necrosis is involved in the initial necrotic cell death, we examined the effect of necroptosis and ferroptosis inhibition by administering inhibitors to wild-type mice in the CDE diet model. In addition, necroptosis was evaluated using mixed lineage kinase domain-like protein (MLKL) knockout mice, which is lacking in a terminal executor of necroptosis. Consequently, necroptosis inhibition failed to block the onset of necrotic cell death, while ferroptosis inhibition protected hepatocytes from necrotic death almost completely, and suppressed the subsequent infiltration of immune cells and inflammatory reaction. Furthermore, the amount of oxidized phosphatidylethanolamine, which is involved in ferroptosis pathway, was increased in the liver sample of the CDE diet-fed mice. These findings suggest that hepatic ferroptosis plays an important role as the trigger for initiating inflammation in steatohepatitis and may be a therapeutic target for preventing the onset of steatohepatitis.
RETRACTED ARTICLE: miR-381 modulates human bone mesenchymal stromal cells (BMSCs) osteogenesis via suppressing Wnt signaling pathway during atrophic nonunion development
Authors: Long Haitao , Zhu Yong , Lin Zhangyuan , Wan Jun , Cheng Liang , Zeng Min , Tang Yifu , Zhao Ruibo 
Published: June 2019

AbstractThe osteogenic differentiation of human bone mesenchymal stromal cells (BMSCs) has been considered as a central issue in fracture healing. Wnt signaling could promote BMSC osteogenic differentiation through inhibiting PPARγ. During atrophic nonunion, Wnt signaling-related factors, WNT5A and FZD3 proteins, were significantly reduced, along with downregulation of Runx2, ALP, and Collagen I and upregulation of PPARγ. Here, we performed a microarray analysis to identify differentially expressed miRNAs in atrophic nonunion tissues that were associated with Wnt signaling through targeting related factors. Of upregulated miRNAs, miR-381 overexpression could significantly inhibit the osteogenic differentiation in primary human BMSCs while increase in PPARγ protein level. Through binding to the 3′UTR of WNT5A and FZD3, miR-381 modulated the osteogenic differentiation via regulating β-catenin nucleus translocation. Moreover, PPARγ, an essential transcription factor inhibiting osteogenic differentiation, could bind to the promoter region of miR-381 to activate its expression. Taken together, PPARγ-induced miR-381 upregulation inhibits the osteogenic differentiation in human BMSCs through miR-381 downstream targets, WNT5A and FZD3, and β-catenin nucleus translocation in Wnt signaling. The in vivo study also proved that inhibition of miR-381 promoted the fracture healing. Our finding may provide a novel direction for atrophic nonunion treatment.
Mitotically heritable effects of BMAA on striatal neural stem cell proliferation and differentiation
Authors: Pierozan Paula , Karlsson Oskar 
Published: June 2019

AbstractThe widespread environmental contaminant β-methylamino-L-alanine (BMAA) is a developmental neurotoxicant that can induce long-term learning and memory deficits. Studies have shown high transplacental transfer of 3H-BMAA and a significant uptake in fetal brain. Therefore, more information on how BMAA may influence growth and differentiation of neural stem cells is required for assessment of the risk to the developing brain. The aim of this study was to investigate direct and mitotically inherited effects of BMAA exposure using primary striatal neurons and embryonic neural stem cells. The neural stem cells were shown to be clearly more susceptible to BMAA exposure than primary neurons. Exposure to 250 µM BMAA reduced neural stem cell proliferation through apoptosis and G2/M arrest. At lower concentrations (50–100 µM), not affecting cell proliferation, BMAA reduced the differentiation of neural stem cells into astrocytes, oligodendrocytes, and neurons through glutamatergic mechanisms. Neurons that were derived from the BMAA-treated neuronal stem cells demonstrated morphological alterations including reduced neurite length, and decreased number of processes and branches per cell. Interestingly, the BMAA-induced changes were mitotically heritable to daughter cells. The results suggest that early-life exposure to BMAA impairs neuronal stem cell programming, which is vital for development of the nervous system and may result in long-term consequences predisposing for both neurodevelopmental disorders and neurodegenerative disease later in life. More attention should be given to the potential adverse effects of BMAA exposure on brain development.
Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns
Authors: Shetty Amol C. , Jacob Christopher G. , Huang Fang , Li Yao , Agrawal Sonia , Saunders David L. , Lon Chanthap , Fukuda Mark M. , Ringwald Pascal , Ashley Elizabeth A. , Han Kay Thwe , Hlaing Tin Maung , Nyunt Myaing M. , Silva Joana C. , Stewart Kathleen E. , Plowe Christopher V. , O’Connor Timothy D. , Takala-Harrison Shannon ,   Artemisinin Resistance Confirmation, Characterization, and Containment (ARC3), Noedl Harald , Khan Wasif A. ,   Artemisinin Resistance Containment and Elimination (ARCE), Newton Paul , Kyaw Myat P. ,   Tracking Resistance to Artemisinin Collaboration (TRAC), White Nicholas J. , Dondorp Arjen M. , Day Nicholas P. , Woodrow Charles J. , Dhorda Mehul , Faiz M. Abul , Fairhurst Rick M. , Lim Pharath , Tripura Rupam , Mayxay Mayfong , Htut Ye , Nosten Francois , Phyo Aung Pyae , Pukrittayakamee Sasithon , Hien Tran Tinh , Nhien Nguyen Thanh Thuy , Mokuolu Olugbenga A. , Fanello Caterina I. , Onyamboko Marie A. 
Published: June 2019

AbstractEstimates of Plasmodium falciparum migration may inform strategies for malaria elimination. Here we elucidate fine-scale parasite population structure and infer recent migration across Southeast Asia using identity-by-descent (IBD) approaches based on genome-wide single nucleotide polymorphisms called in 1722 samples from 54 districts. IBD estimates are consistent with isolation-by-distance. We observe greater sharing of larger IBD segments between artemisinin-resistant parasites versus sensitive parasites, which is consistent with the recent spread of drug resistance. Our IBD analyses reveal actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination, as well as asymmetrical migration identifying potential sources and sinks of migrating parasites.
Force-driven reversible liquid–gas phase transition mediated by elastic nanosponges
Authors: Nomura Keita , Nishihara Hirotomo , Yamamoto Masanori , Gabe Atsushi , Ito Masashi , Uchimura Masanobu , Nishina Yuta , Tanaka Hideki , Miyahara Minoru T. , Kyotani Takashi 
Published: June 2019

AbstractNano-confined spaces in nanoporous materials enable anomalous physicochemical phenomena. While most nanoporous materials including metal-organic frameworks are mechanically hard, graphene-based nanoporous materials possess significant elasticity and behave as nanosponges that enable the force-driven liquid–gas phase transition of guest molecules. In this work, we demonstrate force-driven liquid–gas phase transition mediated by nanosponges, which may be suitable in high-efficiency heat management. Compression and free-expansion of the nanosponge afford cooling upon evaporation and heating upon condensation, respectively, which are opposite to the force-driven solid–solid phase transition in shape-memory metals. The present mechanism can be applied to green refrigerants such as H2O and alcohols, and the available latent heat is at least as high as 192 kJ kg−1. Cooling systems using such nanosponges can potentially achieve high coefficients of performance by decreasing the Young’s modulus of the nanosponge.
Analysis of whole Y-chromosome sequences reveals the Japanese population history in the Jomon period
Authors: Watanabe Yusuke , Naka Izumi , Khor Seik-Soon , Sawai Hiromi , Hitomi Yuki , Tokunaga Katsushi , Ohashi Jun 
Published: June 2019

AbstractThe Jomon and the Yayoi are considered to be the two major ancestral populations of the modern mainland Japanese. The Jomon people, who inhabited mainland Japan, admixed with Yayoi immigrants from the Asian continent. To investigate the population history in the Jomon period (14,500–2,300 years before present [YBP]), we analyzed whole Y-chromosome sequences of 345 Japanese males living in mainland Japan. A phylogenetic analysis of East Asian Y chromosomes identified a major clade (35.4% of mainland Japanese) consisting of only Japanese Y chromosomes, which seem to have originated from indigenous Jomon people. A Monte Carlo simulation indicated that ~70% of Jomon males had Y chromosomes in this clade. The Bayesian skyline plots of 122 Japanese Y chromosomes in the clade detected a marked decrease followed by a subsequent increase in the male population size from around the end of the Jomon period to the beginning of the Yayoi period (2,300 YBP). The colder climate in the Late to Final Jomon period may have resulted in critical shortages of food for the Jomon people, who were hunter-gatherers, and the rice farming introduced by Yayoi immigrants may have helped the population size of the Jomon people to recover.
Recombinant production, purification, crystallization, and structure analysis of human transforming growth factor β2 in a new conformation
Authors: del Amo-Maestro Laura , Marino-Puertas Laura , Goulas Theodoros , Gomis-Rüth F. Xavier 
Published: June 2019

AbstractTransforming growth factor β is a disulfide-linked dimeric cytokine that occurs in three highly related isoforms (TGFβ1–TGFβ3) engaged in signaling functions through binding of cognate TGFβ receptors. To regulate this pathway, the cytokines are biosynthesized as inactive pro-TGFβs with an N-terminal latency-associated protein preceding the mature moieties. Due to their pleiotropic implications in physiology and pathology, TGFβs are privileged objects of in vitro studies. However, such studies have long been limited by the lack of efficient human recombinant expression systems of native, glycosylated, and homogenous proteins. Here, we developed pro-TGFβ2 production systems based on human Expi293F cells, which yielded >2 mg of pure histidine- or Strep-tagged protein per liter of cell culture. We assayed this material biophysically and in crystallization assays and obtained a different crystal form of mature TGFβ2, which adopted a conformation deviating from previous structures, with a distinct dimeric conformation that would require significant rearrangement for binding of TGFβ receptors. This new conformation may be reversibly adopted by a certain fraction of the mature TGβ2 population and represent a hitherto undescribed additional level of activity regulation of the mature growth factor once the latency-associated protein has been separated.
Simulating human exposure to indoor airborne microplastics using a Breathing Thermal Manikin
Authors: Vianello Alvise , Jensen Rasmus Lund , Liu Li , Vollertsen Jes 
Published: June 2019

AbstractHumans are potentially exposed to microplastics through food, drink, and air. The first two pathways have received quite some scientific attention, while little is known about the latter. We address the exposure of humans to indoor airborne microplastics using a Breathing Thermal Manikin. Three apartments were investigated, and samples analysed through FPA-µFTIR-Imaging spectroscopy followed by automatic analyses down to 11 µm particle size. All samples were contaminated with microplastics, with concentrations between 1.7 and 16.2 particles m−3. Synthetic fragments and fibres accounted, on average, for 4% of the total identified particles, while nonsynthetic particles of protein and cellulose constituted 91% and 4%, respectively. Polyester was the predominant synthetic polymer in all samples (81%), followed by polyethylene (5%), and nylon (3%). Microplastics were typically of smaller size than nonsynthetic particles. As the identified microplastics can be inhaled, these results highlight the potential direct human exposure to microplastic contamination via indoor air.
Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum
Authors: van de Vossenberg Bart T. L. H. , Warris Sven , Nguyen Hai D. T. , van Gent-Pelzer Marga P. E. , Joly David L. , van de Geest Henri C. , Bonants Peter J. M. , Smith Donna S. , Lévesque C. André , van der Lee Theo A. J. 
Published: June 2019

AbstractSynchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.
Metabolic remodeling of cardiomyocytes identified in phosphoinositide-dependent kinase 1-deficient mice
Authors: Li Chen , Niu Yan , Zheng Hong , Shan Congjia , Chen Qinbo , Yang Zhongzhou , Zhao Liangcai , Yang Changwei , Gao Hongchang 
Published: June 2019

Abstract
Metabolic remodeling plays an essential role in the pathophysiology of heart failure (HF). Many studies have shown that the disruption of phosphoinositide-dependent protein kinase-1 (PDK1) caused severe and lethal HF; however, the metabolic pattern of PDK1 deletion remains ambiguous. 1H nuclear magnetic resonance-based metabolomics was applied to explore the altered metabolic pattern in Pdk1-deficient mice. Principle component analysis showed significant separation as early as 4 weeks of age, and dysfunction of metabolism precedes a morphological change in Pdk1-deficient mice. A time trajectory plot indicated that disturbed metabolic patterns were related to the pathological process of the HF in Pdk1-deficient mice, rather than the age of mice. Metabolic profiles demonstrated significantly increased levels of acetate, glutamate, glutamine, and O-phosphocholine in Pdk1 deletion mice. Levels of lactate, alanine, glycine, taurine, choline, fumarate, IMP, AMP, and ATP were significantly decreased compared with controls. Furthermore, PDK1 knockdown decreased the oxygen consumption rate in H9C2 cells as determined using a Seahorse XF96 Analyzer. These findings imply that the disruption of metabolism and impaired mitochondrial activity might be involved in the pathogenesis of HF with PDK1 deletion.
Plasma properties of suprathermal electrons near comet 67P/Churyumov-Gerasimenko with Rosetta
Authors: Myllys M. , Henri P. , Galand M. , Heritier K. L. , Gilet N. , Goldstein R. , Eriksson A. I. , Johansson F. , Deca J. 
Published: June 2019

Context. The Rosetta spacecraft escorted comet 67P/Churyumov-Gerasimenko from 2014 to September 2016. The mission provided in situ observations of the cometary plasma during different phases of the cometary activity, which enabled us to better understand its evolution as a function of heliocentric distance.
Aims. In this study, different electron populations, called warm and hot, observed by the Ion and Electron Sensor (IES) of the Rosetta Plasma Consortium (RPC) are investigated near the comet during the escorting phase of the Rosetta mission.
Methods. The estimates for the suprathermal electron densities and temperatures were extracted using IES electron data by fitting a double-kappa function to the measured velocity distributions. The fitting results were validated using observations from other RPC instruments. We give upgraded estimates for the warm and hot population densities compared to values previously shown in literature.
Results. The fitted density and temperature estimates for both electron populations seen by IES are expressed as a function of heliocentric distance to study their evolution with the cometary activity. In addition, we studied the dependence between the electron properties and cometocentric distance.
Conclusions. We observed that when the neutral outgassing rate of the nucleus is high (i.e., near perihelion) the suprathermal electrons are well characterized by a double-kappa distribution. In addition, warm and hot populations show a significant dependence with the heliocentric distance. The populations become clearly denser near perihelion while their temperatures are observed to remain almost constant. Moreover, the warm electron population density is shown to be strongly dependent on the radial distance from the comet. Finally, based on our results we reject the hypothesis that hot electron population seen by IES consists of solely suprathermal (halo) solar wind electrons, while we suggest that the hot electron population mainly consists of solar wind thermal electrons that have undergone acceleration near the comet.