bluuebunny/crossref_metadata_2025 huggingface dataset:
Rethinking the Use of Seabed Sediment Temperature Profiles to Trace Submarine Groundwater Flow
Authors: Kurylyk B. L. , Irvine D. J. , Mohammed A. A. , Bense V. F. , Briggs M. A. , Loder J. W. , Geshelin Y.
Published: May 2018

Submarine groundwater fluxes across the seafloor facilitate important hydrological and biogeochemical exchanges between oceans and seabed sediment, yet few studies have investigated spatially distributed groundwater fluxes in deep‐ocean environments such as continental slopes. Heat has been previously applied as a submarine groundwater tracer using an analytical solution to a heat flow equation assuming steady state conditions and homogeneous thermal conductivity. These assumptions are often violated in shallow seabeds due to ocean bottom temperature changes or sediment property variations. Here heat tracing analysis techniques recently developed for terrestrial settings are applied in concert to examine the influences of groundwater flow, ocean temperature changes, and seabed thermal conductivity variations on deep‐ocean sediment temperature profiles. Temperature observations from the sediment and bottom ocean water on the Scotian Slope off eastern Canada are used to demonstrate how simple thermal methods for tracing groundwater can be employed if more comprehensive techniques indicate that the simplifying assumptions are valid. The spatial distribution of the inferred groundwater fluxes on the slope suggests a downward groundwater flow system with recharge occurring over the upper‐middle slope and discharge on the lower slope. We speculate that the downward groundwater flow inferred on the Scotian Slope is due to density‐driven processes arising from underlying salt domes, in contrast with upward slope systems driven by geothermal convection. Improvements in the design of future submarine hydrogeological studies are proposed for thermal data collection and groundwater flow analysis, including new equations that quantify the minimum detectable flux magnitude for a given sensor accuracy and profile length.
Tomographic Estimation of Exospheric Hydrogen Density Distributions
Authors: Cucho‐Padin G. , Waldrop L.
Published: May 2018

For the past decade, the Lyman‐alpha detectors on board National Aeronautics and Space Administration's Two Wide‐angle Imaging Neutral‐atom Spectrometers (TWINS) mission have obtained routine measurements of solar Lyman‐α photons (121.6 nm) resonantly scattered by atomic hydrogen (H) in the terrestrial exosphere. These data have been used to derive global three‐dimensional (3‐D) models of exospheric H density beyond 3 RE, which are needed to understand various aspects of aeronomy and heliophysics, such as atmospheric chemistry and energetics, magnetospheric energy dissipation, ion‐neutral coupling, and atmospheric evolution through gravitational escape. These empirical distributions are obtained through parametric fitting of assumed functional forms that have little observational justification, thus limiting confidence in conclusions drawn from analysis of the resulting exospheric structure. In this work, we present a new means of global 3‐D reconstruction of exospheric H density through tomographic inversion of the scattered H Lyman‐α emission. Our approach avoids the conventional dependence on ad hoc parametric formulations and, based on the case studies reported here, appears to enable a more accurate characterization of the global structure of the H density in the outer exosphere. We evaluate the bounds of technique feasibility using simulated TWINS data and report new geophysical insights gained from applying this promising new approach to an example of actual TWINS data.
Satellite‐Based Analysis of CO Seasonal and Interannual Variability Over the Amazon Basin
Authors: Deeter M. N. , Martínez‐Alonso S. , Andreae Meinrat O. , Schlager H.
Published: May 2018

The “Measurements of Pollution in the Troposphere” (MOPITT) satellite record is applied to study the geographical and temporal variability of carbon monoxide (CO) from biomass burning in the Amazon Basin. The presented analysis demonstrates the use of satellite observations for interpreting the effects of deforestation and climate on past and future emissions of CO. The study exploits the MOPITT “multispectral” retrieval product which effectively resolves tropospheric CO into two independently measured layers. New validation results based on in situ measurements during the ACRIDICON‐CHUVA aircraft campaign in 2014 are used for bias correction. Contrasting CO monthly climatologies are presented for the Amazon Basin for the lower and upper troposphere (“LT” and “UT”) with an emphasis on the Amazonian dry season. Climatologically, spatial patterns of UT CO over the Amazon Basin appear to be related to both deep convection and anticyclonic flow. Strongly enhanced LT basin‐mean CO concentrations are observed for the dry season months in 2005, 2007, 2010, and 2015, while the record also indicates a decreasing long‐term trend. These observations are consistent with the expected effects of falling deforestation rates since 2004, punctuated by CO spikes in drought years due to large‐scale wildfires.
Hyporheic Exchange Driven by Three‐Dimensional Sandy Bed Forms: Sensitivity to and Prediction from Bed Form Geometry
Authors: Chen Xiaobing , Cardenas M. Bayani , Chen Li
Published: May 2018

Bed form‐driven hyporheic exchange is vital to biogeochemical processes occurring within aquatic sediment. The integrated effects of hyporheic processes in a bed form ultimately impact watershed‐scale water quality. However, much of what is understood regarding bed hyporheic exchange is based on idealized two‐dimensional bed forms despite the prevalence of potentially complex three‐dimensional (3‐D) bed forms in sandy riverbeds. We thus examined the impact of bed form three‐dimensionality on hyporheic exchange. Bed form three‐dimensionality was represented by two groups of geometric parameters: (1) crest planform curvature and (2) transverse and longitudinal wavelength and amplitude. A wide variety of synthetic bed forms was generated based on the geometric parameters. Then, surface flow over and hyporheic flow through each bed form was calculated using a 3‐D multiphysics computational fluid dynamics model implemented across a range of Reynolds Number. We found that hyporheic exchange is sensitive to both types of parameters that determine the bed form three‐dimensionality. Hyporheic exchange is dominated however by the three‐dimensionality caused by out‐of‐phase superimposed sinusoidal surfaces. The results of the complex flow models were synthesized into simple equations for predicting hyporheic flux and bulk residence time based on bed form longitudinal and transverse wavelengths, bed form height, and Reynolds Number.
iASPP–PP1 complex is required for cytokinetic abscission by controlling CEP55 dephosphorylation
Authors: Gao Kun , Zhang Yuanyuan , Shi Qing , Zhang Jianong , Zhang Liang , Sun Huiru , Jiao Dongyue , Zhao Xiayin , Tao Hongru , Wei Youheng , Wang Yuqi , Saiyin Hexige , Zhao Shi-Min , Li Yao , Zhang Pingzhao , Wang Chenji
Published: May 2018

Cytokinesis is the last step of cell division and is concluded by the abscission of the intercellular bridge that connects two daughter cells. The tight regulation of cytokinesis completion is essential because cytokinesis failure is associated with various human diseases. Here, we report that iASPP, a member of the apoptosis-stimulating proteins of p53 (ASPP) family, is required for proper cell division. iASPP depletion results in abnormal midbody structure and failed cytokinesis. We used protein affinity purification methods to identify the functional partners of iASPP. We found that iASPP associates with centrosomal protein of 55 kDa (CEP55), an important cytokinetic abscission regulator. Mechanically, iASPP acts as a PP1-targeting subunit to facilitate the interaction between PP1 and CEP55 and to remove PLK1-mediated Ser436 phosphorylation in CEP55 during late mitosis. The latter step is critical for the timely recruitment of CEP55 to the midbody. The present observations revealed a previously unrecognized function of iASPP in cytokinesis. This function, in turn, likely contributes to the roles of iASPP in tumor development and genetic diseases.
Sphingosine kinase 1-associated autophagy differs between neurons and astrocytes
Authors: Moruno-Manchon Jose F. , Uzor Ndidi-Ese , Ambati Chandrashekar R. , Shetty Vivekananda , Putluri Nagireddy , Jagannath Chinnaswamy , McCullough Louise D. , Tsvetkov Andrey S.
Published: May 2018

Autophagy is a degradative pathway for removing aggregated proteins, damaged organelles, and parasites. Evidence indicates that autophagic pathways differ between cell types. In neurons, autophagy plays a homeostatic role, compared to a survival mechanism employed by starving non-neuronal cells. We investigated if sphingosine kinase 1 (SK1)-associated autophagy differs between two symbiotic brain cell types—neurons and astrocytes. SK1 synthesizes sphingosine-1-phosphate, which regulates autophagy in non-neuronal cells and in neurons. We found that benzoxazine autophagy inducers upregulate SK1 and neuroprotective autophagy in neurons, but not in astrocytes. Starvation enhances SK1-associated autophagy in astrocytes, but not in neurons. In astrocytes, SK1 is cytoprotective and promotes the degradation of an autophagy substrate, mutant huntingtin, the protein that causes Huntington’s disease. Overexpressed SK1 is unexpectedly toxic to neurons, and its toxicity localizes to the neuronal soma, demonstrating an intricate relationship between the localization of SK1’s activity and neurotoxicity. Our results underscore the importance of cell type-specific autophagic differences in any efforts to target autophagy therapeutically.
Genipin alleviates vascular hyperpermeability following hemorrhagic shock by up-regulation of SIRT3/autophagy
Authors: Shumin Cai , Wei Xu , Yunfeng Li , Jiangshui Liang , Youguang Gao , Zhongqing Chen , Tao Li
Published: May 2018

Genipin (GP) is commonly used to treat cardiovascular diseases; however, the protective action of GP against vascular hyperpermeability (VH) has not been reported. We previously reported that intrinsic apoptotic signaling (IAS) is involved in VH following hemorrhagic shock (HS). GP inhibits apoptosis, but the specific mechanism remains unclear. In the present study, we observed that GP protects against HS-induced VH in vitro and in vivo. We report that this protective effect is related to the inhibition of IAS by up-regulation of autophagy via sirtuin 3 (SIRT3). The endothelial cell hyperpermeability induced by HS was enhanced by GP; this was attenuated by 3-methyladenine (3MA), a specific inhibitor of autophagy, indicating the involvement of autophagy. Consistent with these results, we found that 3MA reversed the effects of GP on up-regulation of autophagy, and also diminished the protective effect of GP against IAS activation following HS. Furthermore, knockout of SIRT3 inhibited GP-induced autophagy, indicating the requirement of SIRT3 in the regulation of autophagy by GP. In rats, GP improved HS-induced VH, which was repressed by 3MA and 3-(1H-1,2,3-triazol-4-yl)pyridine (3-TYP), a SIRT3 inhibitor. In conclusion, these findings suggest that autophagy plays a protective effect in VH following HS; the protective effect of autophagy is reinforced by GP, which protects against IAS and VH by up-regulating SIRT3.
Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells
Authors:   The International Stem Cell Initiative, Allison Thomas F. , Andrews Peter W. , Avior Yishai , Barbaric Ivana , Benvenisty Nissim , Bock Christoph , Brehm Jennifer , Brüstle Oliver , Damjanov Ivan , Elefanty Andrew , Felkner Daniel , Gokhale Paul J. , Halbritter Florian , Healy Lyn E. , Hu Tim X. , Knowles Barbara B. , Loring Jeanne F. , Ludwig Tenneille E. , Mayberry Robyn , Micallef Suzanne , Mohamed Jameelah S. , Müller Franz-Josef , Mummery Christine L. , Nakatsuji Norio , Ng Elizabeth S. , Oh Steve K. W. , O’Shea Orla , Pera Martin F. , Reubinoff Benjamin , Robson Paul , Rossant Janet , Schuldt Bernhard M. , Solter Davor , Sourris Koula , Stacey Glyn , Stanley Edouard G. , Suemori Hirofumi , Takahashi Kazutoshi , Yamanaka Shinya
Published: May 2018

The International Stem Cell Initiative compared several commonly used approaches to assess human pluripotent stem cells (PSC). PluriTest predicts pluripotency through bioinformatic analysis of the transcriptomes of undifferentiated cells, whereas, embryoid body (EB) formation in vitro and teratoma formation in vivo provide direct tests of differentiation. Here we report that EB assays, analyzed after differentiation under neutral conditions and under conditions promoting differentiation to ectoderm, mesoderm, or endoderm lineages, are sufficient to assess the differentiation potential of PSCs. However, teratoma analysis by histologic examination and by TeratoScore, which estimates differential gene expression in each tumor, not only measures differentiation but also allows insight into a PSC’s malignant potential. Each of the assays can be used to predict pluripotent differentiation potential but, at this stage of assay development, only the teratoma assay provides an assessment of pluripotency and malignant potential, which are both relevant to the pre-clinical safety assessment of PSCs.
Efficacy of a respiratory syncytial virus vaccine candidate in a maternal immunization model
Authors: Blanco Jorge C. G. , Pletneva Lioubov M. , McGinnes-Cullen Lori , Otoa Raymonde O. , Patel Mira C. , Fernando Lurds R. , Boukhvalova Marina S. , Morrison Trudy G.
Published: May 2018

Respiratory syncytial virus (RSV) is the most common cause of bronchiolitis in infants. Maternal immunization is an option to increase maternal antibody levels and protect infants from infection. Here we assess the efficacy of virus-like particle (VLP) vaccine candidates containing stabilized pre-fusion (pre-F) or post-fusion (post-F) conformations of the RSV F protein and the attachment RSV G protein in a maternal immunization model using cotton rats. VLP vaccines containing RSV F and G proteins strongly boost pre-existing RSV immunity in dams preventing their perinatal drop in immunity. Boosting is stronger for the pre-F VLP than for the post-F VLP or purified subunit F protein vaccines, giving an advantage on mothers’ protection. VLP immunization of dams provides significant protection to pups from RSV challenge and reduced pulmonary inflammation. Collectively, our results show that a VLP vaccine with RSV F and G proteins is safe and effective for maternal and adult vaccination.
B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation
Authors: Barwick Benjamin G. , Scharer Christopher D. , Martinez Ryan J. , Price Madeline J. , Wein Alexander N. , Haines Robert R. , Bally Alexander P. R. , Kohlmeier Jacob E. , Boss Jeremy M.
Published: May 2018

B cells provide humoral immunity by differentiating into antibody-secreting plasma cells, a process that requires cellular division and is linked to DNA hypomethylation. Conversely, little is known about how de novo deposition of DNA methylation affects B cell fate and function. Here we show that genetic deletion of the de novo DNA methyltransferases Dnmt3a and Dnmt3b (Dnmt3-deficient) in mouse B cells results in normal B cell development and maturation, but increased cell activation and expansion of the germinal center B cell and plasma cell populations upon immunization. Gene expression is mostly unaltered in naive and germinal center B cells, but dysregulated in Dnmt3-deficient plasma cells. Differences in gene expression are proximal to Dnmt3-dependent DNA methylation and chromatin changes, both of which coincide with E2A and PU.1-IRF composite-binding motifs. Thus, de novo DNA methylation limits B cell activation, represses the plasma cell chromatin state, and regulates plasma cell differentiation.
Estrogen-related receptor gamma functions as a tumor suppressor in gastric cancer
Authors: Kang Myoung-Hee , Choi Hyunji , Oshima Masanobu , Cheong Jae-Ho , Kim Seokho , Lee Jung Hoon , Park Young Soo , Choi Hueng-Sik , Kweon Mi-Na , Pack Chan-Gi , Lee Ju-Seog , Mills Gordon B. , Myung Seung-Jae , Park Yun-Yong
Published: May 2018

The principle factors underlying gastric cancer (GC) development and outcomes are not well characterized resulting in a paucity of validated therapeutic targets. To identify potential molecular targets, we analyze gene expression data from GC patients and identify the nuclear receptor ESRRG as a candidate tumor suppressor. ESRRG expression is decreased in GC and is a predictor of a poor clinical outcome. Importantly, ESRRG suppresses GC cell growth and tumorigenesis. Gene expression profiling suggests that ESRRG antagonizes Wnt signaling via the suppression of TCF4/LEF1 binding to the CCND1 promoter. Indeed, ESRRG levels are found to be inversely correlated with Wnt signaling-associated genes in GC patients. Strikingly, the ESRRG agonist DY131 suppresses cancer growth and represses the expression of Wnt signaling genes. Our present findings thus demonstrate that ESRRG functions as a negative regulator of the Wnt signaling pathway in GC and is a potential therapeutic target for this cancer.
The CRISPR tool kit for genome editing and beyond
Authors: Adli Mazhar
Published: May 2018

CRISPR is becoming an indispensable tool in biological research. Once known as the bacterial immune system against invading viruses, the programmable capacity of the Cas9 enzyme is now revolutionizing diverse fields of medical research, biotechnology, and agriculture. CRISPR-Cas9 is no longer just a gene-editing tool; the application areas of catalytically impaired inactive Cas9, including gene regulation, epigenetic editing, chromatin engineering, and imaging, now exceed the gene-editing functionality of WT Cas9. Here, we will present a brief history of gene-editing tools and describe the wide range of CRISPR-based genome-targeting tools. We will conclude with future directions and the broader impact of CRISPR technologies.
Solvent-assisted programming of flat polymer sheets into reconfigurable and self-healing 3D structures
Authors: Yang Yang , Terentjev Eugene M. , Wei Yen , Ji Yan
Published: May 2018

It is extremely challenging, yet critically desirable to convert 2D plastic films into 3D structures without any assisting equipment. Taking the advantage of solvent-induced bond-exchange reaction and elastic-plastic transition, shape programming of flat vitrimer polymer sheets offers a new way to obtain 3D structures or topologies, which are hard for traditional molding to achieve. Here we show that such programming can be achieved with a pipette, a hair dryer, and a bottle of solvent. The polymer used here is very similar to the commercial epoxy, except that a small percentage of a specific catalyst is involved to facilitate the bond-exchange reaction. The programmed 3D structures can later be erased, reprogrammed, welded with others, and healed again and again, using the same solvent-assisted technique. The 3D structures can also be recycled by hot-pressing into new sheets, which can still be repeatedly programmed.
Tissue and cellular rigidity and mechanosensitive signaling activation in Alexander disease
Authors: Wang Liqun , Xia Jing , Li Jonathan , Hagemann Tracy L. , Jones Jeffrey R. , Fraenkel Ernest , Weitz David A. , Zhang Su-Chun , Messing Albee , Feany Mel B.
Published: May 2018

Glial cells have increasingly been implicated as active participants in the pathogenesis of neurological diseases, but critical pathways and mechanisms controlling glial function and secondary non-cell autonomous neuronal injury remain incompletely defined. Here we use models of Alexander disease, a severe brain disorder caused by gain-of-function mutations in GFAP, to demonstrate that misregulation of GFAP leads to activation of a mechanosensitive signaling cascade characterized by activation of the Hippo pathway and consequent increased expression of A-type lamin. Importantly, we use genetics to verify a functional role for dysregulated mechanotransduction signaling in promoting behavioral abnormalities and non-cell autonomous neurodegeneration. Further, we take cell biological and biophysical approaches to suggest that brain tissue stiffness is increased in Alexander disease. Our findings implicate altered mechanotransduction signaling as a key pathological cascade driving neuronal dysfunction and neurodegeneration in Alexander disease, and possibly also in other brain disorders characterized by gliosis.
Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages
Authors: Bunnik Evelien M. , Cook Kate B. , Varoquaux Nelle , Batugedara Gayani , Prudhomme Jacques , Cort Anthony , Shi Lirong , Andolina Chiara , Ross Leila S. , Brady Declan , Fidock David A. , Nosten Francois , Tewari Rita , Sinnis Photini , Ay Ferhat , Vert Jean-Philippe , Noble William Stafford , Le Roch Karine G.
Published: May 2018

The development of malaria parasites throughout their various life cycle stages is coordinated by changes in gene expression. We previously showed that the three-dimensional organization of the Plasmodium falciparum genome is strongly associated with gene expression during its replication cycle inside red blood cells. Here, we analyze genome organization in the P. falciparum and P. vivax transmission stages. Major changes occur in the localization and interactions of genes involved in pathogenesis and immune evasion, host cell invasion, sexual differentiation, and master regulation of gene expression. Furthermore, we observe reorganization of subtelomeric heterochromatin around genes involved in host cell remodeling. Depletion of heterochromatin protein 1 (PfHP1) resulted in loss of interactions between virulence genes, confirming that PfHP1 is essential for maintenance of the repressive center. Our results suggest that the three-dimensional genome structure of human malaria parasites is strongly connected with transcriptional activity of specific gene families throughout the life cycle.
Emergent superconductivity in an iron-based honeycomb lattice initiated by pressure-driven spin-crossover
Authors: Wang Yonggang , Ying Jianjun , Zhou Zhengyang , Sun Junliang , Wen Ting , Zhou Yannan , Li Nana , Zhang Qian , Han Fei , Xiao Yuming , Chow Paul , Yang Wenge , Struzhkin Viktor V. , Zhao Yusheng , Mao Ho-kwang
Published: May 2018

The discovery of iron-based superconductors (FeSCs), with the highest transition temperature (Tc) up to 55 K, has attracted worldwide research efforts over the past ten years. So far, all these FeSCs structurally adopt FeSe-type layers with a square iron lattice and superconductivity can be generated by either chemical doping or external pressure. Herein, we report the observation of superconductivity in an iron-based honeycomb lattice via pressure-driven spin-crossover. Under compression, the layered FePX3 (X = S, Se) simultaneously undergo large in-plane lattice collapses, abrupt spin-crossovers, and insulator-metal transitions. Superconductivity emerges in FePSe3 along with the structural transition and vanishing of magnetic moment with a starting Tc ~ 2.5 K at 9.0 GPa and the maximum Tc ~ 5.5 K around 30 GPa. The discovery of superconductivity in iron-based honeycomb lattice provides a demonstration for the pursuit of transition-metal-based superconductors via pressure-driven spin-crossover.
Daily rhythmicity in coastal microbial mats
Authors: Hörnlein Christine , Confurius-Guns Veronique , Stal Lucas J. , Bolhuis Henk
Published: May 2018

Cyanobacteria are major primary producers in coastal microbial mats and provide biochemical energy, organic carbon, and bound nitrogen to the mat community through oxygenic photosynthesis and dinitrogen fixation. In order to anticipate the specific requirements to optimize their metabolism and growth during a day-and-night cycle, Cyanobacteria possess a unique molecular timing mechanism known as the circadian clock that is well-studied under laboratory conditions but little is known about its function in a natural complex community. Here, we investigated daily rhythmicity of gene expression in a coastal microbial mat community sampled at 6 time points during a 24-h period. In order to identify diel expressed genes, meta-transcriptome data was fitted to periodic functions. Out of 24,035 conserved gene transcript clusters, approximately 7% revealed a significant rhythmic expression pattern. These rhythmic genes were assigned to phototrophic micro-eukaryotes, Cyanobacteria but also to Proteobacteria and Bacteroidetes. Analysis of MG-RAST annotated genes and mRNA recruitment analysis of two cyanobacterial and three proteobacterial microbial mat members confirmed that homologs of the cyanobacterial circadian clock genes were also found in other bacterial members of the microbial mat community. These results suggest that various microbial mat members other than Cyanobacteria have their own molecular clock, which can be entrained by a cocktail of Zeitgebers such as light, temperature or metabolites from neighboring species. Hence, microbial mats can be compared to a complex organism consisting of multiple sub-systems that have to be entrained in a cooperative way such that the corpus functions optimally.
Critical amino acids for the insecticidal activity of Vip3Af from Bacillus thuringiensis: Inference on structural aspects
Authors: Banyuls N. , Hernández-Rodríguez C. S. , Van Rie J. , Ferré J.
Published: May 2018

Vip3 vegetative insecticidal proteins from Bacillus thuringiensis are an important tool for crop protection against caterpillar pests in IPM strategies. While there is wide consensus on their general mode of action, the details of their mode of action are not completely elucidated and their structure remains unknown. In this work the alanine scanning technique was performed on 558 out of the total of 788 amino acids of the Vip3Af1 protein. From the 558 residue substitutions, 19 impaired protein expression and other 19 substitutions severely compromised the insecticidal activity against Spodoptera frugiperda. The latter 19 substitutions mainly clustered in two regions of the protein sequence (amino acids 167–272 and amino acids 689–741). Most of these substitutions also decreased the activity to Agrotis segetum. The characterisation of the sensitivity to proteases of the mutant proteins displaying decreased insecticidal activity revealed 6 different band patterns as evaluated by SDS-PAGE. The study of the intrinsic fluorescence of most selected mutants revealed only slight shifts in the emission peak, likely indicating only minor changes in the tertiary structure. An in silico modelled 3D structure of Vip3Af1 is proposed for the first time.
Distinguishing mirtrons from canonical miRNAs with data exploration and machine learning methods
Authors: Rorbach Grzegorz , Unold Olgierd , Konopka Bogumil M.
Published: May 2018

Mirtrons are non-canonical microRNAs encoded in introns the biogenesis of which starts with splicing. They are not processed by Drosha and enter the canonical pathway at the Exportin-5 level. Mirtrons are much less evolutionary conserved than canonical miRNAs. Due to the differences, canonical miRNA predictors are not applicable to mirtron prediction. Identification of differences is important for designing mirtron prediction algorithms and may help to improve the understanding of mirtron functioning. So far, only simple, single-feature comparisons were reported. These are insensitive to complex feature relations. We quantified miRNAs with 25 features and showed that it is impossible to distinguish the two miRNA species using simple thresholds on any single feature. However, when using the Principal Component Analysis mirtrons and canonical miRNAs are grouped separately. Moreover, several methodologically diverse machine learning classifiers delivered high classification performance. Using feature selection algorithms we found features (e.g. bulges in the stem region), previously reported divergent in two classes, that did not contribute to improving classification accuracy, which suggests that they are not biologically meaningful. Finally, we proposed a combination of the most important features (including Guanine content, hairpin free energy and hairpin length) which convey a specific pattern, crucial for identifying mirtrons.
Generation of ultrahigh field by micro-bubble implosion
Authors: Murakami M. , Arefiev A. , Zosa M. A.
Published: May 2018

Breaking the 100-MeV barrier for proton acceleration will help elucidate fundamental physics and advance practical applications from inertial confinement fusion to tumour therapy. Herein we propose a novel concept of bubble implosions. A bubble implosion combines micro-bubbles and ultraintense laser pulses of 1020–1022 W cm−2 to generate ultrahigh fields and relativistic protons. The bubble wall protons undergo volumetric acceleration toward the centre due to the spherically symmetric Coulomb force and the innermost protons accumulate at the centre with a density comparable to the interior of a white dwarf. Then an unprecedentedly high electric field is formed, which produces an energetic proton flash. Three-dimensional particle simulations confirm the robustness of Coulomb-imploded bubbles, which behave as nano-pulsars with repeated implosions and explosions to emit protons. Current technologies should be sufficient to experimentally verify concept of bubble implosions.
Chemical and structural analysis on magnetic tunnel junctions using a decelerated scanning electron beam
Authors: Jackson Edward , Sun Mingling , Kubota Takahide , Takanashi Koki , Hirohata Atsufumi
Published: May 2018

Current information technology relies on the advancement of nanofabrication techniques. For instance, the latest computer memories and hard disk drive read heads are designed with a 12 nm node and 20 nm wide architectures, respectively. With matured nanofabrication processes, a yield of such nanoelectronic devices is typically up to about 90%. To date the yield has been compensated with redundant hardware and software error corrections. In the latest memories, approximately 5% redundancy and parity bits for error corrections are used, which increase the total production cost of the devices. This means the yield directly affects the device costs. It is hence critical to increase the yield in nanofabrication. In this paper, we have applied our recently developed method to image buried interfaces in combination with chemical analysis to evaluate magnetic tunnel junctions and have revealed their different magnetoresistance ratios caused by the presence of materials formed at the junction edges. The formation of these materials can be avoided by optimising the junction patterning process to remove residual carbon introduced from resist. Our imaging method with chemical analysis have demonstrated a significant potential for the improvement of junction performance, resulting in higher yields. This can be used as a quality assurance tool in a nanoelectronic device production line.
Non-alcoholic fatty liver disease incidence, remission and risk factors among a general Chinese population with a 6-year follow-up
Authors: Wu Jing , He Shumei , Xu Hongqin , Chi Xiumei , Sun Jie , Wang Xiaomei , Gao Xiuzhu , Wu Ruihong , Shao Mingbai , Zhao Heng , Jia Jing , Wang Chunyan , Niu Junqi
Published: May 2018

This study aimed to investigate the incidence, remission and risk factors of non-alcoholic fatty liver disease (NAFLD) among a general population with a 6-year follow-up. In total, 691 individuals from the general population in Jilin, China aged 20–75 years participated in two independent cross-sectional surveys carried out in 2007 and 2013. After excluding patients with alcoholism, viral hepatitis and other liver diseases, 646 individuals were finally enrolled in our study. Of the 646 subjects, 512 did not have NAFLD at baseline, while 134 did. Of the 512 individuals without NAFLD at baseline, 188 (36.7%) developed NAFLD during the six-year follow-up period. The baseline body mass index (BMI, OR = 1.49, 1.36–1.64), high-density lipoprotein cholesterol level(HDL-C) (OR = 0.35, 0.16–0.76) and weight gain (OR = 1.22, 1.16–1.29) were independent predictors for NAFLD incidence. Of the 134 subjects with NAFLD at baseline, 33 (24.6%) had no evidence of NAFLD after 6 years. Males (OR = 4.85, 1.98–11.92) and baseline BMI levels (OR = 0.81, 0.70–0.94) were associated with NAFLD remission. Among the general population, the incidence of NAFLD mainly depended on baseline weight and weight gain. Subjects with mild baseline weights and male subjects were prone to NAFLD remission.
New birthweight percentiles by sex and gestational age in Southern China and its comparison with the INTERGROWTH-21st Standard
Authors: Yao Fei , Miao Huazhang , Li Bing , Wu Yuntao , Zhao Qingguo
Published: May 2018

We first showed the sex- and gestational age (week)-specific birthweight distributions from primiparous and multiparous mothers. Birthweight percentiles were created by using the Lambda Mu Sigma (LMS) method. We established the birthweight percentiles in Southern China and provide clinicians and researchers with up-to-date population norms of birthweight percentiles. Then we use the data from Birth Certificate System between Jan 1st, 2017 and Oct 31st, 2017, which included 1,245,364 live births to calculate SGA and LGA ratio by these three birthweight references- the new INTERGROWTH-21st standard, China’s 2015 research standard and our birthweight percentiles. The overall prevalence of SGA estimated by our standards, the China’s 2015 research standards and INTERGROWTH-21st standards, were 10.21%, 12.93% and 7.98%, respectively, whereas the overall prevalence of LGA was 9.88%, 4.48% and 8.37%, respectively.
Pilot-scale study on catalytic ozonation of bio-treated dyeing and finishing wastewater using recycled waste iron shavings as a catalyst
Authors: Ma Jieting , Chen Yunlu , Nie Jianxin , Ma Luming , Huang Yuanxing , Li Liang , Liu Yan , Guo Zhigang
Published: May 2018

A pilot scale reactor with an effective volume of 2.93 m3 was built in-situ and run in both batch and continuous modes to investigate the removal for organic pollutants in bio-treated dyeing and finishing wastewater by heterogeneous catalytic ozonation under neutral pH with waste iron shavings as a catalyst. Experimental results showed that both running modes were able to reduce the chemical oxygen demand (COD) from 132–148 mg/L to a level below the discharge criteria (<80 mg/L) within 15–30 mins under several conditions. Specifically, significantly organic removal was observed with COD, soluble COD (sCOD) and dissolved organic carbon (DOC) decreased from the initial 165, 93 and 76 mg/L to 54, 28 and 16 mg/L respectively, when treated by 10.2 g-O3/min of ozone dosage at a hydraulic retention time of 30 mins under continuous mode. 80% proteins and 85% polysaccharides were removed with a decrease in their contribution to sCOD from 69% to 43%. Mineralization as well as conversion of high molecular organic compounds was observed through Gas Chromatography-Mass Spectrometer (GC-MS) & Liquid Chromatography-Mass Spectrometer (LC-MS) analysis, which led to a decrease of inhibitory effect from 29% to 25%, suggesting a reduction in the acute toxicity.
Intrauterine smoke exposure deregulates lung function, pulmonary transcriptomes, and in particular insulin-like growth factor (IGF)-1 in a sex-specific manner
Authors: Dehmel Stefan , Nathan Petra , Bartel Sabine , El-Merhie Natalia , Scherb Hagen , Milger Katrin , John-Schuster Gerrit , Yildirim Ali Oender , Hylkema Machteld , Irmler Martin , Beckers Johannes , Schaub Bianca , Eickelberg Oliver , Krauss-Etschmann Susanne
Published: May 2018

Prenatal exposure to tobacco smoke is a significant risk-factor for airway disease development. Furthermore, the high prevalence of pregnant smoking women requires the establishment of strategies for offspring lung protection. Therefore, we here aimed to understand the molecular mechanism of how prenatal smoke exposure affects fetal lung development. We used a mouse model recapitulating clinical findings of prenatally exposed children, where pregnant mice were exposed to smoke until c-section or spontaneous delivery, and offspring weight development and lung function was monitored. Additionally, we investigated pulmonary transcriptome changes in fetal lungs (GD18.5) by mRNA/miRNA arrays, network analyses and qPCR. The results demonstrated that prenatally exposed mice showed intrauterine and postnatal growth retardation, and impaired lung function. 1340 genes and 133 miRNAs were found to be significantly dysregulated by in utero smoke exposure, and we identified Insulin-like growth factor 1 (Igf1) as a top hierarchical node in a network analysis. Moreover, Igf1 mRNA was increased in female murine offspring and in prenatally exposed children. These findings suggest that prenatal smoking is associated with a dysregulation of several genes, including Igf1 in a sex-specific manner. Thus, our results could represent a novel link between smoke exposure, abberant lung development and impaired lung function.
The cell wall hydrolase Pmp23 is important for assembly and stability of the division ring in Streptococcus pneumoniae
Authors: Jacq Maxime , Arthaud Christopher , Manuse Sylvie , Mercy Chryslène , Bellard Laure , Peters Katharina , Gallet Benoit , Galindo Jennifer , Doan Thierry , Vollmer Waldemar , Brun Yves V. , VanNieuwenhze Michael S. , Di Guilmi Anne Marie , Vernet Thierry , Grangeasse Christophe , Morlot Cecile
Published: May 2018

Bacterial division is intimately linked to synthesis and remodeling of the peptidoglycan, a cage-like polymer that surrounds the bacterial cell, providing shape and mechanical resistance. The bacterial division machinery, which is scaffolded by the cytoskeleton protein FtsZ, includes proteins with enzymatic, structural or regulatory functions. These proteins establish a complex network of transient functional and/or physical interactions which preserve cell shape and cell integrity. Cell wall hydrolases required for peptidoglycan remodeling are major contributors to this mechanism. Consistent with this, their deletion or depletion often results in morphological and/or division defects. However, the exact function of most of them remains elusive. In this work, we show that the putative lysozyme activity of the cell wall hydrolase Pmp23 is important for proper morphology and cell division in the opportunistic human pathogenStreptococcus pneumoniae. Our data indicate that active Pmp23 is required for proper localization of the Z-ring and the FtsZ-positioning protein MapZ. In addition, Pmp23 localizes to the division site and interacts directly with the essential peptidoglycan synthase PBP2x. Altogether, our data reveal a new regulatory function for peptidoglycan hydrolases.
Falls and Recurrent Falls among Adults in A Multi-ethnic Asian Population: The Singapore Epidemiology of Eye Diseases Study
Authors: Dai Wei , Tham Yih-Chung , Chee Miao-Li , Tan Nicholas Y. Q. , Wong Kah-Hie , Majithia Shivani , Sabanayagam Charumathi , Lamoureux Ecosse , Wong Tien-Yin , Cheng Ching-Yu
Published: May 2018

We evaluated the rate and risk factors associated with falls and recurrent falls in a multi-ethnic Asian population. 10,009 participants aged ≥40 years (mean[SD] age = 58.9[10.4] years) underwent clinical examinations and completed interviewer-administered questionnaires. Participants who self-reported at least one fall or ≥2 falls in past 12 months were defined as fallers and recurrent fallers, respectively. Age-standardized rates for falls and recurrent falls were 13.8% (95%CI, 13.1–14.6%) and 4.6% (95%CI, 4.2–5.1%), respectively. Multivariable analyses showed older age (OR = 1.20; 95%CI, 1.11–1.30), female gender (OR = 1.79; 95%CI, 1.54–2.07), diabetes (OR = 1.22; 95%CI, 1.07–1.40), cardiovascular disease (CVD, OR = 1.37; 95%CI, 1.14–1.65), ≥3 systemic comorbidities (OR = 1.35; 95%CI, 1.09–1.67), lower European Quality of Life-5 Dimensions (EQ-5D) score (OR = 1.36; 95%CI, 1.29–1.44), alcohol consumption (OR = 1.41, 95%CI, 1.11–1.78) and presenting visual impairment (VI, OR = 1.23; 95%CI, 1.02–1.47) were associated with falls. For recurrent falls, female gender (OR = 2.27; 95%CI, 1.75–2.94), diabetes (OR = 1.28; 95%CI, 1.03–1.61), CVD (OR = 2.00; 95%CI, 1.53–2.62), ≥3 systemic comorbidities (OR = 1.69; 95%CI, 1.19–2.39), lower EQ-5D score (OR = 1.47; 95%CI, 1.35–1.59), living in 1–2 room public flat (OR = 1.57; 95%CI, 1.05–2.33), monthly income <2000 Singapore Dollar (OR = 1.62; 95%CI, 1.13–2.31), alcohol consumption (OR = 1.81, 95%CI, 1.23–2.66) and presenting VI (OR = 1.34; 95%CI, 1.01–1.79) were significant risk factors. These findings will be useful for the formulation of fall prevention programs.
Elucidation of inhibitory effects on metastatic sentinel lymph nodes of breast cancer during One-Step Nucleic Acid Amplification
Authors: Horimoto Yoshiya , Tanabe Masahiko , Kazuno Saiko , Miura Yoshiki , Mogushi Kaoru , Sonoue Hiroshi , Arakawa Atsushi , Kajino Kazunori , Kobayashi Toshiyuki , Saito Mitsue
Published: May 2018

One-step nucleic acid amplification (OSNA) is an established method for intraoperative diagnosis of breast cancer metastasis in sentinel lymph nodes, based on quantification of CK19 mRNA, specific to breast epithelial cells. Inhibitors interfere with the PCR amplification process of PCR. Thus, OSNA, based on gene amplification without RNA purification, might be impacted by numerous factors persisting in a sample, and thereby potentially acting as PCR inhibitors. However, neither the characteristics of breast cancers showing inhibitory effects during OSNA, nor any of the possible inhibitors, have as yet been identified. Inhibitory effects detected during OSNA in 72 metastatic lymph nodes and the patients’ clinicopathological features were examined. Left-over OSNA samples were analyzed with mass spectrometry to identify proteins possibly acting as inhibitors. Most tumors showed inhibitory effects, though to varying degrees. Large tumor, young age and high tumor-infiltrating lymphocyte counts were related to stronger inhibitory effects. Proteome analysis revealed elevations in RPB9 protein and EIF2 signaling upregulation in samples showing strong inhibitory effects. Tumors showing strong inhibitory effects had clinically relevant characteristics, including large size and extensive tumor-infiltrating lymphocyte involvement. Identifying inhibitors in OSNA might provide new insights into breast cancer biology as well as advancing the current technology.
Voltage-dependent Ca2+ channels promote branching morphogenesis of salivary glands by patterning differential growth
Authors: Kim J. M. , Choi S. , Lee S. W. , Park K.
Published: May 2018

Branching morphogenesis is a crucial part of early developmental processes in diverse organs, but the detailed mechanism of this morphogenic event remains to be elucidated. Here we introduce an unknown mechanism leading to branching morphogenesis using mouse embryonic organotypic cultures with time-lapse live imaging. We found spatially expressed L-type voltage-dependent Ca2+ channels (VDCCs) in the peripheral layers of developing epithelial buds and identified the VDCCs as a core signaling mediator for patterning branching architecture. In this process, differential growth in peripheral layers by VDCC-induced ERK activity promoted cleft formation through an epithelial buckling-folding mechanism. Our findings reveal an unexpected role of VDCCs in developmental processes, and address a fundamental question regarding the initial process of branching morphogenesis.
Apple pomace improves gut health in Fisher rats independent of seed content
Authors: Ravn-Haren Gitte , Krath Britta N. , Markowski Jarosław , Poulsen Morten , Hansen Max , Kołodziejczyk Krzysztof , Kosmala Monika , Dragsted Lars O.
Published: May 2018

Apple pomace with seeds had no adverse effects in a 4-week feeding study in rats and retained its functionality.
Optical bandgap modelling from the structural arrangement of carbon nanotubes
Authors: Butler Timothy P. , Rashid Ijaz , Montelongo Yunuen , Amaratunga Gehan A. J. , Butt Haider
Published: May 2018

Spectral studies on the periodic arrays of vertically-aligned multiwalled carbon nanotube arrays.
Enhanced DNA detection using a multiple pulse pumping scheme with time-gating (MPPTG)
Authors: Kimball Joseph D. , Maliwal Badri , Raut Sangram L. , Doan Hung , Nurekeyev Zhangatay , Gryczynski Ignacy , Gryczynski Zygmunt
Published: May 2018

Fluorescence signal enhancement induced by the binding of intercalators to DNA has been broadly utilized in various DNA detection methods.
An asymmetric fitting function for condensed-phase Raman spectroscopy
Authors: Korepanov Vitaly I. , Sedlovets Daria M.
Published: May 2018

An asymmetric fitting function is designed by the damped perturbation of a Voigt profile and tested on systems with different natures of asymmetry.
A PET based fluorescent chemosensor with real time application in monitoring formaldehyde emissions from plywood
Authors: Gangopadhyay Ankita , Maiti Kalipada , Ali Syed Samim , Pramanik Ajoy Kumar , Guria Uday Narayan , Samanta Sandip Kumar , Sarkar Ripon , Datta Pallab , Mahapatra Ajit Kumar
Published: May 2018

A simple, robust fluorescent chemodosimeter capable of detecting nanomolar levels of formaldehyde with applicability in monitoring formaldehyde emissions from plywood.
Inhibition of homophilic dimerization and disruption of cell adhesion by P-cadherin-specific small molecules from SPR-based assays
Authors: Senoo Akinobu , Nagatoishi Satoru , Moberg Anna , Babol Linnea Nygren , Mitani Tomoya , Tashima Takumi , Kudo Shota , Tsumoto Kouhei
Published: May 2018

Our SPR-based screening identified a compound which was able to inhibit cell adhesion mediated by homophilic dimerization of P-cadherin.
Visible-light-induced alkoxyl radical generation for inert chemical bond cleavage/functionalization
Authors: Jia Kunfang , Chen Yiyun
Published: May 2018

The recent advancements in inert C(sp3)–H, C(sp3)–C(sp3), and C(sp3)–X bond cleavage/functionalization by visible-light-induced alkoxyl radical generation are discussed.
Proton triggered circularly polarized luminescence in orthogonal- and co-assemblies of chiral gelators with achiral perylene bisimide
Authors: Han Dongxue , Han Jianlei , Huo Shengwei , Qu Zuoming , Jiao Tifeng , Liu Minghua , Duan Pengfei
Published: May 2018

Acid–base exposure switched circularly polarized luminescence was achieved in a coassembled gel which is composed of a chiral gelator and achiral perylene bisimide.
Solvent dependent pathway complexity and seeded supramolecular polymerization
Authors: Ghosh Goutam , Ghosh Suhrit
Published: May 2018

cNDI-1 exhibits an off-pathway aggregate in cyclic hydrocarbon (MCH) but produces a helical supramolecular polymer in linear alkane (decane) by well-defined J-aggregation.
Role of tailor-made additives in controlling vapour growth asymmetry along the polar axis of α-resorcinol crystals: a molecular-scale study
Authors: Singh M. K. , Banerjee Arup
Published: May 2018

The role of different tailor-made additives and conformers of resorcinol have been investigated to elucidate the mechanism of unidirectional vapour growth of α-resorcinol crystal. Our results show the growth anisotropy is linked with the surface stabilization of the slow growing face.
A theoretical study on the structures and electronic and magnetic properties of new boron nitride composite nanosystems by depositing superhalogen Al13on the surface of nanosheets/nanoribbons
Authors: Shen Xiaopeng , Yu Guangtao , Zhang Chenghui , Wang Ting , Huang Xuri , Chen Wei
Published: May 2018

Superhalogen Al13and BN nanosystems are used to construct new composite Al13@BN nanostructures with the intriguing electronic and magnetic properties.
DFT insight into the effect of potassium on the adsorption, activation and dissociation of CO2 over Fe-based catalysts
Authors: Nie Xiaowa , Meng Linlin , Wang Haozhi , Chen Yonggang , Guo Xinwen , Song Chunshan
Published: May 2018

DFT study uncovers the promoting effect of potassium on the adsorption and dissociation of CO2 over Fe-based catalysts.