bluuebunny/crossref_metadata_2025 huggingface dataset:
Bored and online: Reasons for using social media, problematic social networking site use, and behavioral outcomes across the transition from adolescence to emerging adulthood
Authors: Stockdale Laura A. , Coyne Sarah M.
Published: January 2020

Introduction

The current study examined motivations for social networking site use across three years during the transition from late adolescence to emerging adulthood. While research has been conducted examining reasons for social networking site usage and behavior, the clear majority have focused on samples of undergraduate college students and are cross‐sectional.

Methods

Changes in motivations for using social networking sites were examined in relation to problematic social networking site use and several behavioral and mental health outcomes in a sample of adolescents over three years.

Results

Using social networking sites to connect with others was relatively stable over a three‐year period. However, using social networking sites to seek information increased from late adolescence to emerging adulthood and was not related to any negative outcomes across three years. Using social networking sites to alleviate boredom also increased over time. Initial levels of social media use to alleviate boredom were associated with problematic social networking site use, financial stress, anxiety, and empathy at year three. Increases in using social networking sites to socially connect over time was related to problematic social networking site use, anxiety, delinquency, and empathy at year three. Using social networking sites for any reason was not related to depressive symptoms over three years.

Conclusions

The current study supports the growing body of literature suggesting that using social networking sites to alleviate boredom and socially connect, may place individuals at increased risk for developing pathological tendencies and patterns of behavior towards social networking sites.
Re-evaluating Political Trust: The Impact of Survey Nonresponse in Rural China
Authors: Ratigan Kerry , Rabin Leah
Published: January 2020

Has survey nonresponse caused scholars to overestimate political trust in China? We analyse item nonresponse for sensitive questions on trust in government from our original survey of villagers conducted in China in 2012. We also analyse nonresponse in four other comparable surveys conducted in China between 1993 and 2014. We examine the association between nonresponse to politically sensitive questions and individual characteristics such as sex, level of education, Party membership and cosmopolitanism. We find that less privileged groups may be underrepresented in survey data generally. We find mixed results regarding the association between cosmopolitanism and nonresponse. We conclude that our understanding of political trust in China has been compromised by high rates of item nonresponse, leading to artificially high estimates of trust in the centre and exaggerated accounts of the gap between trust in central and local leaders.
Disentangling multiproblem behavior in male young adults: A cluster analysis
Authors: Zijlmans Josjan , van Duin Laura , Jorink Maaike , Marhe Reshmi , Luijks Marie-Jolette A. , Crone Matty , Popma Arne , Bevaart Floor
Published: January 2020

Multiproblem young adults present with major problems across key life domains, but empirical studies investigating the nature of multiproblem behavior in accordance to ecobiodevelopmental theory are scarce. To address this gap, we performed a cluster analysis on indicators spanning the key life domains addiction, mental health, social network, and justice. In a large sample (N = 680) of multiproblem young adults, we identified five subgroups labeled “severe with alcohol and cannabis problems” (4.3%), “severe with cannabis problems” (25.6%), “severe without alcohol or drug problems” (33.2%), “moderate with mental health problems” (22.9%), and “moderate without mental health problems” (14.0%). There were large differences between the severe and moderate groups in terms of childhood risk factors such as emotional and physical abuse, concerning baseline functioning such as comorbid disorders and aggressive behavior, and in the outcome measure of violent offending. Our findings indicate that multiproblem young adult behavior clusters within profiles that differ according to the severity and nature of problems. Investing in screening for clustered problems may be beneficial for early problem differentiation and selection of appropriate intervention before and during treatment programs.
GPS‐Based LEO Orbits Referenced to the Earth's Center of Mass
Authors: Couhert Alexandre , Delong Nicolas , Ait‐Lakbir Hanane , Mercier Flavien
Published: January 2020

Global Navigation Satellite System satellite clock solutions of the International Global Navigation Satellite System Service are aligned to the International Terrestrial Reference Frame origin. This strategy is not sufficient to model correctly the Low Earth Orbit (LEO) Global Positioning System (GPS) measurements, because the geocenter motion is not taken into account for the ground station positions in these solutions. In order to be consistent with the dynamic motion of a LEO satellite, and also with the other measurement systems where the geocenter motion can be modeled (e.g., Satellite Laser Ranging and Doppler Orbitography and Radiopositioning Integrated by Satellite), it is necessary to take into account or mitigate the miscentering effect of the constellation solution. In this paper, we use a parametric model representing the reference network translations, and this model can be adjusted in the OSTM/Jason‐2 and Jason‐3 LEO satellites orbit determination.
Rupture Of Veined Granite In Polyaxial Compression: Insights From Three‐Dimensional Discrete Element Method Modeling
Authors: Shang Junlong
Published: January 2020

Granite formations have been frequently involved in subsurface energy‐related activities such as radioactive waste disposal, oil, and gas storage. This is principally because of their mechanical stability, low permeability, and high corrosion resistance. These favorable properties, however, can be compromised by the addition of mineral veins, which tend to occur ubiquitously in upper crustal rock formations. Evaluation of the impact of veins on the integrity and rupture characteristics of granite, especially under true triaxial stresses, is therefore important yet currently underemphasized. This study examines the rupture of veined granite in polyaxial compression via a discrete element method model. In the model with soft veins, the rupture is localized along the fabricated inclined veins (45° relative to the horizontal with strike running in the σ2 direction) under low confining stresses (σ2 < 67 MPa); in contrast, a combined rupture of veins and granite matrix is observed when σ2 is increased to 141.6 MPa. Shear sliding along the inclined veins is revealed by examining the displacement field. Shear‐induced volumetric dilation is suspected in the soft‐veined models in relatively low confining stresses (σ2 < 67 MPa) with sliding and dilation behavior apparently suppressed at σ2 = 141.6 MPa. Hard veins impede local rupture, resulting in conjugate shear bands. The well‐recognized σ2 effect is observed for the hard‐veined models, while no pronounced σ2 effect is noticed for the soft‐veined models. This study also reveals that vein thickness has a negligible impact on rupture characteristics, which is however profoundly affected by vein orientation.
Spatial Variations of Subsurface Chlorophyll Maxima During Thermal Stratification in a Large, Deep Subtropical Reservoir
Authors: Liu Miao , Zhang Yunlin , Shi Kun , Melack John , Zhang Yibo , Zhou Yongqiang , Zhu Mengyuan , Zhu Guangwei , Wu Zhixu , Liu Mingliang
Published: January 2020

Subsurface chlorophyll maxima (SCM) are found in stratified lakes, reservoirs, and oceans. Spatial variations of the SCM magnitude, depth, and thickness during stratification and related factors were examined in a large, deep subtropical reservoir, Lake Qiandaohu. Significant spatial differences in the SCM parameters were found throughout the lake as thermal stratification developed in the late spring of 2014. SCM depth and thickness were positively correlated with euphotic depth and mixed layer depth but negatively correlated with epilimnetic nutrient concentrations. SCM magnitude was negatively correlated with euphotic depth and mixed layer depth and positively correlated with epilimnetic nutrient concentrations. Seasonal variations in SCM differed among subregions of the lake, which were related to seasonal differences in environmental parameters. SCM (averaging 66.2 mg/m2 in spring and 96.4 mg/m2 in summer) accounted for about 82% of the total areal chlorophyll of the water column (Tchl), and the SCM magnitude was better correlated with Tchl than the surface chlorophyll concentration. This study contributes to understanding of factors causing spatial variations in of SCM in the deep subtropical lakes.
3‐D Architecture and Plio‐Quaternary Evolution of the Paola Basin: Insights Into the Forearc of the Tyrrhenian‐Ionian Subduction System
Authors: Corradino M. , Pepe F. , Bertotti G. , Picotti V. , Monaco C. , Nicolich R.
Published: January 2020

Using seismic reflection profiles and bathymetric data, we analyzed the stratigraphy and tectonics of the Paola Basin, providing information on the dynamic of the forearc of the Tyrrhenian‐Ionian subduction system. The Paola Basin is a NNW‐SSE trending syncline, bounded by the Coastal Chain to the east and the Paola Anticline to the west. It hosts up to 5.2 km thick Plio‐Quaternary deposits, most of them supplied from Apenninic/Sila entry points and transported by longshore currents. The total subsidence reaches a value of ∼5 km. The sedimentary load varies from 60% to 75% of the total subsidence. The Pliocene to Lower Pleistocene sedimentary infill of the syncline displays a strata growth geometry consistent with a continuous rotation of the eastern limb of the Paola Anticline. Crustal folding can explain both the tectonic subsidence of the Paola Basin and the uplift of the Paola Anticline. To the east of the basin, Late Pliocene to Early Pleistocene growth of the central sector of the Coastal Chain led to the definition of the Paola and Crati basins, previously connected in a larger proto basin. The trench‐parallel component of the plate movement was accommodated by a strike‐slip zone, with associated releasing and restraining bends coinciding with the Paola Anticline. The bathymetric expression of the strike‐slip zone consists of structural highs and depressions that overall form the Paola Ridge. Since the Middle Pleistocene, the growth of the Paola Anticline and Paola Basin came to an end and extensional tectonics controlled the evolution of the forearc region.
NBS1 is required for SPO11-linked DNA double-strand break repair in male meiosis
Authors: Zhang Bin , Tang Zhenghui , Li Lejun , Lu Lin-Yu
Published: January 2020

DNA double-strand breaks (DSBs) pose a serious threat to genomic stability. Paradoxically, hundreds of programed DSBs are generated by SPO11 in meiotic prophase, which are exclusively repaired by homologous recombination (HR) to promote obligate crossover between homologous chromosomes. In somatic cells, MRE11-RAD50-NBS1 (MRN) complex-dependent DNA end resection is a prerequisite for HR repair, especially for DSBs that are covalently linked with proteins or chemicals. Interestingly, all meiotic DSBs are linked with SPO11 after being generated. Although MRN complex’s function in meiotic DSB repair has been established in lower organisms, the role of MRN complex in mammalian meiotic DSB repair is not clear. Here, we show that MRN complex is essential for repairing meiotic SPO11-linked DSBs in male mice. In male germ cells, conditional inactivation of NBS1, a key component of MRN complex, causes dramatic reduction of DNA end resection and defective HR repair in meiotic prophase. NBS1 loss severely disrupts chromosome synapsis, generates abnormal chromosome structures, and eventually leads to meiotic arrest and male infertility in mice. Unlike in somatic cells, the recruitment of NBS1 to SPO11-linked DSB sites is MDC1-independent but requires other phosphorylated proteins. Collectively, our study not only reveals the significance of MRN complex in repairing meiotic DSBs but also discovers a unique mechanism that recruits MRN complex to SPO11-linked DSB sites.
Increase in global emissions of HFC-23 despite near-total expected reductions
Authors: Stanley K. M. , Say D. , Mühle J. , Harth C. M. , Krummel P. B. , Young D. , O’Doherty S. J. , Salameh P. K. , Simmonds P. G. , Weiss R. F. , Prinn R. G. , Fraser P. J. , Rigby M.
Published: January 2020

Under the Kigali Amendment to the Montreal Protocol, new controls are being implemented to reduce emissions of HFC-23 (CHF$${}_{3}$$3), a by-product during the manufacture of HCFC-22 (CHClF$${}_{2}$$2). Starting in 2015, China and India, who dominate global HCFC-22 production (75% in 2017), set out ambitious programs to reduce HFC-23 emissions. Here, we estimate that these measures should have seen global emissions drop by 87% between 2014 and 2017. Instead, atmospheric observations show that emissions have increased and in 2018 were higher than at any point in history (15.9 $$\pm \ 0.9\ {\rm{{Gg}}\ {{{yr}}}^{-1}}$$±0.9Ggyr−1). Given the magnitude of the discrepancy between expected and observation-inferred emissions, it is likely that the reported reductions have not fully materialized or there may be substantial unreported production of HCFC-22, resulting in unaccounted-for HFC-23 by-product emissions. The difference between reported and observation-inferred estimates suggests that an additional ~309 Tg $${{\rm{CO}}}_{2}$$CO2-equivalent emissions were added to the atmosphere between 2015 and 2017.
Author Correction: Chemokine receptor trafficking coordinates neutrophil clustering and dispersal at wounds in zebrafish
Authors: Coombs Caroline , Georgantzoglou Antonios , Walker Hazel A. , Patt Julian , Merten Nicole , Poplimont Hugo , Busch-Nentwich Elisabeth M. , Williams Sarah , Kotsi Christina , Kostenis Evi , Sarris Milka
Published: January 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Quantifying electron-transfer in liquid-solid contact electrification and the formation of electric double-layer
Authors: Lin Shiquan , Xu Liang , Chi Wang Aurelia , Wang Zhong Lin
Published: January 2020

Contact electrification (CE) has been known for more than 2600 years but the nature of charge carriers and their transfer mechanisms still remain poorly understood, especially for the cases of liquid–solid CE. Here, we study the CE between liquids and solids and investigate the decay of CE charges on the solid surfaces after liquid–solid CE at different thermal conditions. The contribution of electron transfer is distinguished from that of ion transfer on the charged surfaces by using the theory of electron thermionic emission. Our study shows that there are both electron transfer and ion transfer in the liquid–solid CE. We reveal that solutes in the solution, pH value of the solution and the hydrophilicity of the solid affect the ratio of electron transfers to ion transfers. Further, we propose a two-step model of electron or/and ion transfer and demonstrate the formation of electric double-layer in liquid–solid CE.
Hepatitis Delta Virus histone mimicry drives the recruitment of chromatin remodelers for viral RNA replication
Authors: Abeywickrama-Samarakoon Natali , Cortay Jean-Claude , Sureau Camille , Müller Susanne , Alfaiate Dulce , Guerrieri Francesca , Chaikuad Apirat , Schröder Martin , Merle Philippe , Levrero Massimo , Dény Paul
Published: January 2020

Hepatitis Delta virus (HDV) is a satellite of Hepatitis B virus with a single-stranded circular RNA genome. HDV RNA genome synthesis is carried out in infected cells by cellular RNA polymerases with the assistance of the small hepatitis delta antigen (S-HDAg). Here we show that S-HDAg binds the bromodomain (BRD) adjacent to zinc finger domain 2B (BAZ2B) protein, a regulatory subunit of BAZ2B-associated remodeling factor (BRF) ISWI chromatin remodeling complexes. shRNA-mediated silencing of BAZ2B or its inactivation with the BAZ2B BRD inhibitor GSK2801 impairs HDV replication in HDV-infected human hepatocytes. S-HDAg contains a short linear interacting motif (SLiM) KacXXR, similar to the one recognized by BAZ2B BRD in histone H3. We found that the integrity of the S-HDAg SLiM sequence is required for S-HDAg interaction with BAZ2B BRD and for HDV RNA replication. Our results suggest that S-HDAg uses a histone mimicry strategy to co-activate the RNA polymerase II-dependent synthesis of HDV RNA and sustain HDV replication.
Manipulating spin polarization of titanium dioxide for efficient photocatalysis
Authors: Pan Lun , Ai Minhua , Huang Chenyu , Yin Li , Liu Xiang , Zhang Rongrong , Wang Songbo , Jiang Zheng , Zhang Xiangwen , Zou Ji-Jun , Mi Wenbo
Published: January 2020

Photocatalysis has been regarded as a promising strategy for hydrogen production and high-value-added chemicals synthesis, in which the activity of photocatalyst depends significantly on their electronic structures, however the effect of electron spin polarization has been rarely considered. Here we report a controllable method to manipulate its electron spin polarization by tuning the concentration of Ti vacancies. The characterizations confirm the emergence of spatial spin polarization among Ti-defected TiO2, which promotes the efficiency of charge separation and surface reaction via the parallel alignment of electron spin orientation. Specifically, Ti0.936O2, possessing intensive spin polarization, performs 20-fold increased photocatalytic hydrogen evolution and 8-fold increased phenol photodegradation rates, compared with stoichiometric TiO2. Notably, we further observed the positive effect of external magnetic fields on photocatalytic activity of spin-polarized TiO2, attributed to the enhanced electron-spin parallel alignment. This work may create the opportunity for tailoring the spin-dependent electronic structures in metal oxides.
Dataset of human medial temporal lobe neurons, scalp and intracranial EEG during a verbal working memory task
Authors: Boran Ece , Fedele Tommaso , Steiner Adrian , Hilfiker Peter , Stieglitz Lennart , Grunwald Thomas , Sarnthein Johannes
Published: January 2020

We present an electrophysiological dataset recorded from nine subjects during a verbal working memory task. Subjects were epilepsy patients undergoing intracranial monitoring for the localization of epileptic seizures. Subjects performed a modified Sternberg task in which the encoding of memory items, maintenance, and recall were temporally separated. The dataset includes simultaneously recorded scalp EEG with the 10–20 system, intracranial EEG (iEEG) recorded with depth electrodes, waveforms and spike times of neurons recorded in the medial temporal lobe, and localization information on the depth electrodes. Subject characteristics and information on each trial (set size, match/mismatch, correct/incorrect, response, and response time) are given. For technical validation of data, we provide spike sorting quality metrics and the spectra of iEEG and scalp EEG signals. This dataset enables the investigation of working memory by providing simultaneous scalp EEG and iEEG recordings, which can be used for connectivity analysis, along with hard-to-obtain neuronal recordings from humans.
Optimally Sharp Energy Filtering of Quantum Particles via Homogeneous Planar Inclusions
Authors: Valagiannopoulos Constantinos
Published: January 2020

Some of the most influential players from academia and industry have recently expressed concrete interest for quantum engineering applications, especially for new concepts in controlling and processing the quantum signals traveling into condensed matter. An important operation when manipulating particle beams behaving as matter waves concerns filtering with respect to their own energy; such an objective can be well-served by a single planar inclusion of specific size and texture embedded into suitable background. A large number of inclusion/host combinations from realistic materials are tried and the optimally sharp resonance regimes, which correspond to performance limits for such a simplistic structure, are carefully identified. These results may inspire efforts towards the generalization of the adopted approach and the translation of sophisticated inverse design techniques, already successfully implemented for nanophotonic setups, into quantum arena.
Preparation and Characterization of Optimized Hydrochar from Paper Board Mill Sludge
Authors: Oumabady Sadish , S. Paul Sebastian , Kamaludeen Sara P. B. , Ramasamy Mahendiran , Kalaiselvi P. , Parameswari E.
Published: January 2020

The amount of Paper Board Mill Effluent Treatment Plant Sludge (PBM-ETPS) dumped from paper mills are huge and its conversion into hydrochar for the purpose of energy has broad prospects. This study investigated the optimum conditions for the production of PBM-ETPS derived hydrochar (PBM-ETPSH) through Reponse Surface Methodology (RSM) for more surface area and pore volume with minimal hydrogen to carbon (H/C) and oxygen to carbon (O/C) ratios. The PBM-ETPSH had higher heating value (HHV) of 18.39 MJ kg−1 with fixed carbon percentage of 15.6. Our results showed a reduction in H/C (35.05%) and O/C (43.7%) ratios confirming the coalification of optimized PBM-ETPSH. Thermogravimetric investigations of blending PBM-ETPSH with coal in 1:1 ratio increased its HHV to 22.25 MJ kg−1 making it suitable as an energy alternative for paper mills.
MicroRNA and mRNA interactions coordinate the immune response in non-lethal heat stressed Litopenaeus vannamei against AHPND-causing Vibrio parahaemolyticus
Authors: Boonchuen Pakpoom , Maralit Benedict A. , Jaree Phattarunda , Tassanakajon Anchalee , Somboonwiwat Kunlaya
Published: January 2020

While Vibrio parahaemolyticus (VPAHPND) has been identified as the cause of early mortality syndrome (EMS) or acute hepatopancreatic necrosis disease (AHPND) in shrimp, mechanisms of host response remain unknown. Understanding these processes is important to improve farming practices because this understanding will help to develop methods to enhance shrimp immunity. Pre-treatment of shrimp with 5-minute chronic non-lethal heat stress (NLHS) for 7 days was found to significantly increase Litopenaeus vannamei survival against VPAHPND infection. To elucidate the mechanism involved, mRNA and miRNA expression profiles from the hemocyte of L. vannamei challenged with VPAHPND after NLHS with corresponding control conditions were determined by RNA-Seq. A total of 2,664 mRNAs and 41 miRNAs were differentially expressed after the NLHS treatment and VPAHPND challenge. A miRNA-mRNA regulatory network of differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs) was subsequently constructed and the interactions of DEMs in regulating the NLHS-induced immune-related pathways were identified. Transcriptomic data revealed that miRNA and mRNA interactions contribute to the modulation of NLHS-induced immune responses, such as the prophenoloxidase-activating system, hemocyte homeostasis, and antimicrobial peptide production, and these responses enhance VPAHPND resistance in L. vannamei.
Analysis of the co-translational assembly of the fungal fatty acid synthase (FAS)
Authors: Fischer Manuel , Joppe Mirko , Mulinacci Barbara , Vollrath Ronnald , Konstantinidis Kosta , Kötter Peter , Ciccarelli Luciano , Vonck Janet , Oesterhelt Dieter , Grininger Martin
Published: January 2020

The yeast fatty acid synthase (FAS) is a barrel-shaped 2.6 MDa complex. Upon barrel-formation, two multidomain subunits, each more than 200 kDa large, intertwine to form a heterododecameric complex that buries 170,000 Å2 of protein surface. In spite of the rich knowledge about yeast FAS in structure and function, its assembly remained elusive until recently, when co-translational interaction of the β-subunit with the nascent α-subunit was found to initiate assembly. Here, we characterize the co-translational assembly of yeast FAS at a molecular level. We show that the co-translationally formed interface is sensitive to subtle perturbations, so that the exchange of two amino acids located in the emerging interface can prevent assembly. On the other hand, assembly can also be initiated via the co-translational interaction of the subunits at other sites, which implies that this process is not strictly site or sequence specific. We further highlight additional steps in the biogenesis of yeast FAS, as the formation of a dimeric subunit that orchestrates complex formation and acts as platform for post-translational phosphopantetheinylation. The presented data supports the understanding of the recently discovered prevalence of eukaryotic complexes for co-translational assembly, and is valuable for further harnessing FAS in the biotechnological production of aliphatic compounds.
A surrogate weighted mean ensemble method to reduce the uncertainty at a regional scale for the calculation of potential evapotranspiration
Authors: Yoo Byoung Hyun , Kim Junhwan , Lee Byun-Woo , Hoogenboom Gerrit , Kim Kwang Soo
Published: January 2020

We propose a weighted ensemble approach using a surrogate variable. As a case study, the degree of agreement (DOA) statistics for potential evapotranspiration (PET) was determined to compare the ordinary arithmetic mean ensemble (OAME) method and the surrogate weighted mean ensemble (SWME) method for three domains. Solar radiation was used as the surrogate variable to determine the weight values for the ensemble members. Singular vector decomposition with truncation values was used to select five ensemble members for the SWME method. The SWME method tended to have greater DOA statistics for PET than the OAME method with all available models. The distribution of PET values for the SWME method also had greater DOA statistics than that for the OAME method over relatively large spatial extent by month. These results suggest that the SWME method based on the weight value derived from the surrogate variable is suitable for exploiting both diversity and elitism to minimize the uncertainty of PET ensemble data. These findings could contribute to a better design of climate change adaptation options by improving confidence of PET projection data for the assessment of climate change impact on natural and agricultural ecosystems using the SWME method.
Probing thermal transport across amorphous region embedded in a single crystalline silicon nanowire
Authors: Zhao Yunshan , Liu Xiangjun , Rath Ashutosh , Wu Jing , Li Baowen , Zhou WuXing , Xie Guofeng , Zhang Gang , Thong John T. L.
Published: January 2020

While numerous studies have been carried out to characterize heat transport behaviours in various crystalline silicon nanostructures, the corresponding characteristics of amorphous one-dimension system have not been well understood. In this study, we amorphize crystalline silicon by means of helium-ion irradiation, enabling the formation of a completely amorphous region of well-defined length along a single silicon nanowire. Heat conduction across both amorphous region and its crystalline/amorphous interface is characterized by an electron beam heating technique with high measurement spatial resolution. The measured thermal conductivity of the amorphous silicon nanowire appears length-independence with length ranging from ~30 nm to few hundreds nm, revealing the fully diffusons governed heat conduction. Moreover, unlike the size-dependent interfacial thermal conductance at the interface between two one-dimensional crystalline materials, here for the first time, we observe that the interface thermal conductance across the amorphous/crystalline silicon interface is nearly independent of the length of the amorphous region. This unusual independence is further supported by molecular dynamics (MD) simulation in our work. Our results provide experimental and theoretical insight into the nature of interaction between heat carriers in crystalline and amorphous nano-structures and shed new light to design innovative silicon nanowire based devices.
Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii
Authors: Koch Hanna , Germscheid Nora , Freese Heike M. , Noriega-Ortega Beatriz , Lücking Dominik , Berger Martine , Qiu Galaxy , Marzinelli Ezequiel M. , Campbell Alexandra H. , Steinberg Peter D. , Overmann Jörg , Dittmar Thorsten , Simon Meinhard , Wietz Matthias
Published: January 2020

Ecological differentiation between strains of bacterial species is shaped by genomic and metabolic variability. However, connecting genotypes to ecological niches remains a major challenge. Here, we linked bacterial geno- and phenotypes by contextualizing pangenomic, exometabolomic and physiological evidence in twelve strains of the marine bacterium Alteromonas macleodii, illuminating adaptive strategies of carbon metabolism, microbial interactions, cellular communication and iron acquisition. In A. macleodii strain MIT1002, secretion of amino acids and the unique capacity for phenol degradation may promote associations with Prochlorococcus cyanobacteria. Strain 83-1 and three novel Pacific isolates, featuring clonal genomes despite originating from distant locations, have profound abilities for algal polysaccharide utilization but without detrimental implications for Ecklonia macroalgae. Degradation of toluene and xylene, mediated via a plasmid syntenic to terrestrial Pseudomonas, was unique to strain EZ55. Benzoate degradation by strain EC673 related to a chromosomal gene cluster shared with the plasmid of A. mediterranea EC615, underlining that mobile genetic elements drive adaptations. Furthermore, we revealed strain-specific production of siderophores and homoserine lactones, with implications for nutrient acquisition and cellular communication. Phenotypic variability corresponded to different competitiveness in co-culture and geographic distribution, indicating linkages between intraspecific diversity, microbial interactions and biogeography. The finding of “ecological microdiversity” helps understanding the widespread occurrence of A. macleodii and contributes to the interpretation of bacterial niche specialization, population ecology and biogeochemical roles.
Quaternary ice sheets and sea level regression drove divergence in a marine gastropod along Eastern and Western coasts of South America
Authors: Fernández Iriarte P. J. , González-Wevar C. A. , Segovia N. I. , Rosenfeld S. , Hüne M. , Fainburg L. , Nuñez J. D. , Haye P. A. , Poulin E.
Published: January 2020

The southern coastline of South America is a remarkable area to evaluate how Quaternary glacial processes impacted the demography of the near-shore marine biota. Here we present new phylogeographic analyses in the pulmonateSiphonaria lessoniiacross its distribution, from northern Chile in the Pacific to Uruguay in the Atlantic. Contrary to our expectations, populations from the southwestern Atlantic, an area that was less impacted by ice during glacial maxima, showed low genetic diversity and evidence of recent expansion, similar to the patterns recorded in this study across heavily ice-impacted areas in the Pacific Magellan margin. We propose that Atlantic and Pacific shallow marine hard-substrate benthic species were both affected during the Quaternary in South America, but by different processes. At higher latitudes of the southeast Pacific, ice-scouring drastically affectedS. lessoniipopulations compared to non-glaciated areas along the Chile-Peru province where the species was resilient. In the southwest Atlantic,S. lessoniipopulations would have been dramatically impacted by the reduction of near-shore rocky habitat availability as a consequence of glacio-eustatic movements. The increase of gravelly and rocky shore substrates in the southwest Atlantic supports a hypothesis of glacial refugia from where the species recolonized lower latitudes across the Atlantic and Pacific margins. Our results suggest that current patterns of genetic diversity and structure in near-shore marine benthic species do not solely depend on the impact of Quaternary glacial ice expansions but also on the availability of suitable habitats and life-history traits, including developmental mode, bathymetry and the likelihood of dispersal by rafting.
Regulation of Cell Viability and Anti-inflammatory Tristetraprolin Family Gene Expression in Mouse Macrophages by Cottonseed Extracts
Authors: Cao Heping , Sethumadhavan Kandan
Published: January 2020

Bioactive plant extracts have been used for the prevention and treatment of various diseases. One of the major classes of bioactive compounds is plant polyphenols. Cottonseed ethanol extracts were determined by HPLC-MS analysis to be essentially free of toxic gossypol. The objective of this study was to investigate the effect of cottonseed ethanol extracts on the cytotoxicity and regulation of anti-inflammatory tristrataprolin (TTP) family gene expression in mouse cells. MTT, qPCR and immunoblotting assays tested the effects of cottonseed extracts in mouse RAW264.7 macrophages and 3T3-L1 adipocytes. No cytotoxicity effect was observed in macrophages treated with extracts from the coat or kernel of glanded and glandless cottonseed. Similarly, the viability of mouse adipocytes was not affected by cottonseed extracts. In contrast, gossypol and lipopolysaccharides were toxic to macrophages but not adipocytes under high concentration or long time treatment. Cottonseed extracts exhibited modest effect on TTP family gene expression in macrophages but glandless cottonseed coat extract significantly increased TTP mRNA and protein levels with a magnitude similar to cinnamon and green tea polyphenol extract and insulin. These results demonstrated that cottonseed extracts are harmless towards the mouse cells and that glandless cottonseed coat extract stimulates TTP gene expression. We propose that glandless cottonseed is a safe source of plant polyphenols with anti-inflammatory property.
Investigating Chaperonin-Containing TCP-1 subunit 2 as an essential component of the chaperonin complex for tumorigenesis
Authors: Showalter Anne E. , Martini Ana C. , Nierenberg Daniel , Hosang Kristen , Fahmi Naima Ahmed , Gopalan Priya , Khaled Amr S. , Zhang Wei , Khaled Annette R.
Published: January 2020

Chaperonin-containing TCP-1 (CCT or TRiC) is a multi-subunit complex that folds many of the proteins essential for cancer development. CCT is expressed in diverse cancers and could be an ideal therapeutic target if not for the fact that the complex is encoded by eight distinct genes, complicating the development of inhibitors. Few definitive studies addressed the role of specific subunits in promoting the chaperonin’s function in cancer. To this end, we investigated the activity of CCT2 (CCTβ) by overexpressing or depleting the subunit in breast epithelial and breast cancer cells. We found that increasing total CCT2 in cells by 1.3-1.8-fold using a lentiviral system, also caused CCT3, CCT4, and CCT5 levels to increase. Likewise, silencing cct2 gene expression by ~50% caused other CCT subunits to decrease. Cells expressing CCT2 were more invasive and had a higher proliferative index. CCT2 depletion in a syngeneic murine model of triple negative breast cancer (TNBC) prevented tumor growth. These results indicate that the CCT2 subunit is integral to the activity of the chaperonin and is needed for tumorigenesis. Hence CCT2 could be a viable target for therapeutic development in breast and other cancers.
Crustacean remains from the Yuka mammoth raise questions about non-analogue freshwater communities in the Beringian region during the Pleistocene
Authors: Neretina Anna N. , Gololobova Maria A. , Neplyukhina Alisa A. , Zharov Anton A. , Rogers Christopher D. , Horne David J. , Protopopov Albert V. , Kotov Alexey A.
Published: January 2020

Frozen permafrost Pleistocene mammal carcasses with soft tissue remains are subject to intensive study and help elucidate the palaeoenvironment where these animals lived. Here we present an inventory of the freshwater fauna and flora found in a sediment sample from the mummified Woolly Mammoth carcass found in August 2010, from the Oyogos Yar coast near the Kondratievo River in the Laptev Sea region, Sakha (Yakutia) Republic, NE Russia. Our study demonstrates that the waterbody where the carcass was buried could be characterized as a shallow pond or lake inhabited mainly by taxa which are present in this area today, but additionally by some branchiopod crustacean taxa currently absent or unusual in the region although they exist in the arid zone of Eurasia (steppes and semi-deserts). These findings suggest that some “non-analogue” crustacean communities co-existed with the “Mammoth fauna”. Our findings raise questions about the nature of the waterbodies that existed in Beringia during the MIS3 climatic optimum when the mammoth was alive.
Long-term Proton Pump Inhibitor Administration Caused Physiological and Microbiota Changes in Rats
Authors: Yang Yu-Chen S. H. , Chang Hsuen-Wen , Lin I-Hsuan , Chien Li-Nien , Wu Min-Ju , Liu Yun-Ru , Chu Peiguo G. , Xie Guoxiang , Dong Fangcong , Jia Wei , Chang Vincent H. S. , Yen Yun
Published: January 2020

Proton pump inhibitors (PPIs) are used for the long-term treatment of gastroesophageal disorders and the non-prescription medicines for acid reflux. However, there is growing concerns about PPI misuse, overuse and abuse. This study aimed to develop an animal model to examine the effects of long-term use of PPI in vivo. Twenty one Wistar rats were given omeprazole orally or intravenously for 30 days, and caerulein as a positive control. After euthanization, the serum and stool were collected to perform MS-based quantitative analysis of metabolites. We carried out 16S-based profiling of fecal microbiota, assessed the expression of bile acid metabolism regulators and examined the immunopathological characteristics of bile ducts. After long-term PPI exposure, the fecal microbial profile was altered and showed similarity to those observed in high-fat diet studies. The concentrations of several metabolites were also changed in various specimens. Surprisingly, morphological changes were observed in the bile duct, including ductal epithelial proliferation, micropapillary growth of biliary epithelium, focal bile duct stricture formation and bile duct obstruction. These are characteristics of precancerous lesions of bile duct. FXR and RXRα expressions were significantly reduced, which were similar to that observed in cholangiocarcinoma in TCGA and Oncomine databases. We established a novel animal model to examine the effects of long-term use of omeprazole. The gut microbes and metabolic change are consequences of long-term PPI exposure. And the results showed the environment in vivo tends to a high-fat diet. More importantly, we observed biliary epithelial hyperplasia, which is an indicator of a high-fat diet.
A nationwide population-based study to access the risk of metachronous esophageal cancers in head and neck cancer survivors
Authors: Tseng Chao-Ming , Wang Hsi-Hao , Lee Ching-Tai , Tai Chi-Ming , Tseng Cheng-Hao , Chen Chih-Cheng , Tsai Ying-Nan , Chen Tzu-Haw , Hsu Ming-Hung , Wang Chih-Chun , Hwang Tzer-Zen , Wang Hsiu-Po , Wang Wen-Lun
Published: January 2020

How long esophageal screening should be performed for, and on which sub-groups of head and neck cancer (HNC) survivors, remains uncertain. This retrospective study analyzed data from the Taiwan National Health Insurance Research Database from 1999 to 2013. A total of 68,131 newly- diagnosed HNC patients were enrolled. Subjects who received esophageal endoscopic screening within 6 months after their diagnosis date of index HNC were identified. The incidence trends of secondary primary EC were analyzed using a Cochran-Armitage trend test. Among the 9,707 patients who received index esophageal endoscopy screening, 101 (1.0%) cases of synchronous EC were diagnosed. The 5- and 10-year cumulative incidence rates of metachronous ECs were 1.4% and 2.7%, respectively in those with an initial negative index endoscopic finding. Patients with oropharynx or hypopharynx cancers were at significantly higher risk of developing metachronous ECs compared with those with oral or larynx cancers (10-year incidence rate: 3.3% vs. 0.9%, respectively; hazard ratio: 2.15; 95% confidence intervals: 1.57–2.96). Metachronous EC continues to develop in patients with HNC even at 10-years after treatment for primary HNC. HNC patients, especially those with oropharynx or hypopharynx cancer, may require long-term endoscopic surveillance.
HBV X protein mutations affect HBV transcription and association of histone-modifying enzymes with covalently closed circular DNA
Authors: Chong Chun Kong , Cheng Ching Yan Serene , Tsoi Sin Yi Jasmine , Huang Fung-Yu , Liu Fen , Fung James , Seto Wai-Kay , Lai Keane K.-Y. , Lai Ching-Lung , Yuen Man-Fung , Wong Danny Ka-Ho
Published: January 2020

The hepatitis B X protein (HBx) plays a role in the epigenetic regulation of hepatitis B virus (HBV) replication. This study investigated the effects of HBx mutations on HBV transcription and the recruitment of HBx, histone acetyl-transferase P300 and histone deacetylase 1 (HDAC1) to circularized HBV DNA (which resembles covalently closed circular DNA [cccDNA]). Compared with wild type, majority of mutants had lower levels of intracellular HBV RNA (44–77% reduction) and secretory HBsAg (25–81% reduction), and 12 mutants had a reduction in intracellular encapsidated HBV DNA (33–64% reduction). Eight mutants with >70% reduction in HBV RNA and/or HBsAg were selected for chromatin immunoprecipitation analysis. Four HBx mutants with mutations in amino acid residues 55–60 and 121–126 had a lower degree of HBx-cccDNA association than wild type HBx (mean % input: 0.02–0.64% vs. 3.08% in wild type). A reduced association between cccDNA and P300 (mean % input: 0.69–1.81% vs. 3.48% in wild type) and an augmented association with HDAC1 (mean % input: 4.01–14.0% vs. 1.53% in wild type) were detected. HBx amino acid residues 55–60 and 121–126 may play an important role in HBV transcription regulation, via their impeded interaction with cccDNA and altered recruitment of histone modifying enzymes to cccDNA.
Increased blood pressure variability during the subacute phase of ischemic stroke is associated with poor functional outcomes at 3 months
Authors: Naito Hiroyuki , Hosomi Naohisa , Kuzume Daisuke , Nezu Tomohisa , Aoki Shiro , Morimoto Yuko , Kinboshi Masato , Yoshida Takeshi , Shiga Yuji , Kinoshita Naoto , Ueno Hiroki , Noma Kensuke , Yamasaki Masahiro , Maruyama Hirofumi
Published: January 2020

Thus far, it is well known that increased blood pressure variability may exacerbate stroke outcomes. Blood pressure in the acute phase would be influenced by both reactive hypertension to stroke and intrinsic blood pressure reactivity. Thus, we aimed to evaluate the association between blood pressure variability and outcomes at 3 months using ambulatory blood pressure monitoring in ischemic stroke patients in the subacute phase after reactive hypertension subsided. We retrospectively examined 626 consecutive patients with acute ischemic stroke who underwent 24-hour ambulatory blood pressure monitoring during the subacute phase of stroke (median, 9 days from onset). The variability in blood pressure was evaluated by assessing the standard deviation and coefficient of variation of systolic and diastolic blood pressure. The primary outcome was functional status at 3 months. A poor outcome was defined as a modified Rankin scale score of 3 or more and a good outcome as 2 or less. We assessed the functional outcome at 3 months in 497 patients (79.4%). The mean systolic and diastolic blood pressure levels were not associated with functional outcome. The multivariable analysis revealed that increases in the standard deviations of systolic and diastolic blood pressure, coefficient of variation of diastolic blood pressure, and morning blood pressure surge were associated with poor outcome. Blood pressure variability during the subacute phase of ischemic stroke can be a useful prognostic indicator of poor functional outcome at 3 months in patients with acute ischemic stroke.
Proteomic analysis reveals potential factors associated with enhanced EPS production in Streptococcus thermophilus ASCC 1275
Authors: Padmanabhan Aparna , Tong Yin , Wu Qinglong , Lo Clive , Shah Nagendra P.
Published: January 2020

Streptococcus thermophilus ASCC 1275 has two chain length determining genes - epsC and epsD- in its eps gene cluster, and produces two times more EPS in sucrose medium than that in glucose and lactose. Hence, we investigated the influence of sugars (glucose, sucrose and lactose), at log phase (5 h) and stationary phase (10 h), on the global proteomics of S. thermophilus 1275 to understand the differentially expressed proteins (DEPs) during EPS production using isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis. Among 98 DEPs in sucrose medium, most of them were mapped into EPS biosynthesis pathway and other related metabolisms. There was an upregulation of several proteins involved in sugar transport (phosphoenolpyruvate (PEP) phosphotransferase system), EPS assembly (epsG1D) and amino acid metabolism (methionine, cysteine/arginine metabolism) in sucrose medium. This study showed that increased EPS production in S. thermophilus 1275 requires a well-co-ordinated regulation of pathway involved in both EPS assembly and amino acid metabolism along with the availability of sugars. Thus, it provided valuable insights into the biosynthesis and regulation of EPS in S. thermophilus 1275, and potential gene targets for understanding high-EPS strains.
Appearance of cysts and capillary non perfusion areas in diabetic macular edema using two different OCTA devices
Authors: Parravano Mariacristina , Costanzo Eliana , Borrelli Enrico , Sacconi Riccardo , Virgili Gianni , Sadda SriniVas R. , Scarinci Fabio , Varano Monica , Bandello Francesco , Querques Giuseppe
Published: January 2020

The aim of this paper was to distinguish the appearance of cysts and non-perfusion areas (NPAs) in diabetic macular edema (DME) using two different Optical Coherence Tomography Angiography (OCTA) devices. In this study, patients underwent OCTA using the AngioVue XR Avanti Spectral Domain (SD) OCTA and the PLEX Elite 9000 Swept-Source (SS) OCTA. Foveal and extrafoveal regions of interest (ROI), defined as any area with an altered flow signal comparing to the surrounding retina, were selected in superficial and deep capillary plexus (SCP and DCP). ROI reflectivity were classified as hypo-reflective or hyper-reflective. Foveal ROI were analyzed to detect suspended scattering particles in motion (SSPiM). Thirty-seven DME eyes were included. A larger number of ROIs were found in SCP (55 vs 39) and DCP (60 vs 49) using PLEX Elite 9000 vs AngioVue. The majority of ROIs were hypo-reflective with both instruments, while slightly more hyper-reflective ROIs (grey) were detected with the PLEX Elite, more likely to be cysts. The hyporeflective ROIs could be NPAs or cysts with both devices. Moreover, PLEX Elite 9000 identified SSPiM in more foveal ROIs than the AngioVue in the SCP (p = 0.005) and in the DCP (p = 0.027). In conclusion, NPAs and cysts may show variable appearances using different OCTA devices. Hyperreflective ROIs generally correspond to cysts, hyporeflective ROIs can be either cysts or NPAs. The SS-OCTA seems to detect SSPiM more frequently than the SD-OCTA.