bluuebunny/crossref_metadata_2025_split huggingface dataset:
Manganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators
Authors: Wu Miao , McCain J. Scott P. , Rowland Elden , Middag Rob , Sandgren Mats , Allen Andrew E. , Bertrand Erin M. 
Published: August 2019

AbstractIron and light are recognized as limiting factors controlling Southern Ocean phytoplankton growth. Recent field-based evidence suggests, however, that manganese availability may also play a role. Here we examine the influence of iron and manganese on protein expression and physiology in Phaeocystis antarctica, a key Antarctic primary producer. We provide taxon-specific proteomic evidence to show that in-situ Southern Ocean Phaeocystis populations regularly experience stress due to combined low manganese and iron availability. In culture, combined low iron and manganese induce large-scale changes in the Phaeocystis proteome and result in reorganization of the photosynthetic apparatus. Natural Phaeocystis populations produce protein signatures indicating late-season manganese and iron stress, consistent with concurrently observed stimulation of chlorophyll production upon additions of manganese or iron. These results implicate manganese as an important driver of Southern Ocean productivity and demonstrate the utility of peptide mass spectrometry for identifying drivers of incomplete macronutrient consumption.
Microbial carbon use efficiency predicted from genome-scale metabolic models
Authors: Saifuddin Mustafa , Bhatnagar Jennifer M. , Segrè Daniel , Finzi Adrien C. 
Published: August 2019

AbstractRespiration by soil bacteria and fungi is one of the largest fluxes of carbon (C) from the land surface. Although this flux is a direct product of microbial metabolism, controls over metabolism and their responses to global change are a major uncertainty in the global C cycle. Here, we explore an in silico approach to predict bacterial C-use efficiency (CUE) for over 200 species using genome-specific constraint-based metabolic modeling. We find that potential CUE averages 0.62 ± 0.17 with a range of 0.22 to 0.98 across taxa and phylogenetic structuring at the subphylum levels. Potential CUE is negatively correlated with genome size, while taxa with larger genomes are able to access a wider variety of C substrates. Incorporating the range of CUE values reported here into a next-generation model of soil biogeochemistry suggests that these differences in physiology across microbial taxa can feed back on soil-C cycling.
Mild replication stress causes chromosome mis-segregation via premature centriole disengagement
Authors: Wilhelm Therese , Olziersky Anna-Maria , Harry Daniela , De Sousa Filipe , Vassal Helène , Eskat Anja , Meraldi Patrick 
Published: August 2019

AbstractReplication stress, a hallmark of cancerous and pre-cancerous lesions, is linked to structural chromosomal aberrations. Recent studies demonstrated that it could also lead to numerical chromosomal instability (CIN). The mechanism, however, remains elusive. Here, we show that inducing replication stress in non-cancerous cells stabilizes spindle microtubules and favours premature centriole disengagement, causing transient multipolar spindles that lead to lagging chromosomes and micronuclei. Premature centriole disengagement depends on the G2 activity of the Cdk, Plk1 and ATR kinases, implying a DNA-damage induced deregulation of the centrosome cycle. Premature centriole disengagement also occurs spontaneously in some CIN+ cancer cell lines and can be suppressed by attenuating replication stress. Finally, we show that replication stress potentiates the effect of the chemotherapeutic agent taxol, by increasing the incidence of multipolar cell divisions. We postulate that replication stress in cancer cells induces numerical CIN via transient multipolar spindles caused by premature centriole disengagement.
Experimental test of error-tradeoff uncertainty relation using a continuous-variable entangled state
Authors: Liu Yang , Ma Zhihao , Kang Haijun , Han Dongmei , Wang Meihong , Qin Zhongzhong , Su Xiaolong , Peng Kunchi 
Published: August 2019

AbstractHeisenberg’s original uncertainty relation is related to measurement effect, which is different from the preparation uncertainty relation. However, it has been shown that Heisenberg’s error disturbance uncertainty relation is not valid in some cases. We experimentally test the error-tradeoff uncertainty relation by using a continuous-variable Gaussian Einstein–Podolsky–Rosen (EPR)-entangled state. Based on the quantum correlation between the two entangled optical beams, the errors on amplitude and phase quadratures of one EPR optical beam coming from joint measurement are estimated, respectively, which are used to verify the error–tradeoff relation. Especially, the error–tradeoff relation for error-free measurement of one observable is verified in our experiment. We also verify the error–tradeoff relations for nonzero errors and mixed state by introducing loss on one EPR beam. Our experimental results demonstrate that Heisenberg’s error–tradeoff relation is violated in some cases for a continuous-variable system, while the Ozawa’s and Branciard’s relations are valid.
Magnetism and in-gap states of 3d transition metal atoms on superconducting Re
Authors: Schneider Lucas , Steinbrecher Manuel , Rózsa Levente , Bouaziz Juba , Palotás Krisztián , dos Santos Dias Manuel , Lounis Samir , Wiebe Jens , Wiesendanger Roland 
Published: August 2019

AbstractMagnetic atoms on heavy-element superconducting substrates are potential building blocks for realizing topological superconductivity in one- and two-dimensional atomic arrays. Their localized magnetic moments induce so-called Yu-Shiba-Rusinov (YSR) states inside the energy gap of the substrate. In the dilute limit, where the electronic states of the array atoms are only weakly coupled, proximity of the YSR states to the Fermi energy is essential for the formation of topological superconductivity in the band of YSR states. Here, we reveal via scanning tunnel spectroscopy and ab initio calculations of a series of 3d transition metal atoms (Mn, Fe, Co) adsorbed on the heavy-element superconductor Re that the increase of the Kondo coupling and sign change in magnetic anisotropy with d-state filling is accompanied by a shift of the YSR states through the energy gap of the substrate and a crossing of the Fermi level. The uncovered systematic trends enable the identification of the most promising candidates for the realization of topological superconductivity in arrays of similar systems.
AqSolDB, a curated reference set of aqueous solubility and 2D descriptors for a diverse set of compounds
Authors: Sorkun Murat Cihan , Khetan Abhishek , Er Süleyman 
Published: August 2019

AbstractWater is a ubiquitous solvent in chemistry and life. It is therefore no surprise that the aqueous solubility of compounds has a key role in various domains, including but not limited to drug discovery, paint, coating, and battery materials design. Measurement and prediction of aqueous solubility is a complex and prevailing challenge in chemistry. For the latter, different data-driven prediction models have recently been developed to augment the physics-based modeling approaches. To construct accurate data-driven estimation models, it is essential that the underlying experimental calibration data used by these models is of high fidelity and quality. Existing solubility datasets show variance in the chemical space of compounds covered, measurement methods, experimental conditions, but also in the non-standard representations, size, and accessibility of data. To address this problem, we generated a new database of compounds, AqSolDB, by merging a total of nine different aqueous solubility datasets, curating the merged data, standardizing and validating the compound representation formats, marking with reliability labels, and providing 2D descriptors of compounds as a Supplementary Resource.
Brain-behaviour modes of covariation in healthy and clinically depressed young people
Authors: Mihalik Agoston , Ferreira Fabio S. , Rosa Maria J. , Moutoussis Michael , Ziegler Gabriel , Monteiro Joao M. , Portugal Liana , Adams Rick A. , Romero-Garcia Rafael , Vértes Petra E. , Kitzbichler Manfred G. , Váša František , Vaghi Matilde M. , Bullmore Edward T. , Fonagy Peter , Goodyer Ian M. , Jones Peter B. ,   NSPN Consortium, Hauser Tobias , Neufeld Sharon , Clair Michelle St , Whitaker Kirstie , Inkster Becky , Prabhu Gita , Ooi Cinly , Toseeb Umar , Widmer Barry , Bhatti Junaid , Villis Laura , Alrumaithi Ayesha , Birt Sarah , Bowler Aislinn , Cleridou Kalia , Dadabhoy Hina , Davies Emma , Firkins Ashlyn , Granville Sian , Harding Elizabeth , Hopkins Alexandra , Isaacs Daniel , King Janchai , Kokorikou Danae , Maurice Christina , McIntosh Cleo , Memarzia Jessica , Mills Harriet , O’Donnell Ciara , Pantaleone Sara , Scott Jenny , Fearon Pasco , Suckling John , van Harmelen Anne-Laura , Kievit Rogier , Dolan Raymond , Mourão-Miranda Janaina 
Published: August 2019

AbstractUnderstanding how variations in dimensions of psychometrics, IQ and demographics relate to changes in brain connectivity during the critical developmental period of adolescence and early adulthood is a major challenge. This has particular relevance for mental health disorders where a failure to understand these links might hinder the development of better diagnostic approaches and therapeutics. Here, we investigated this question in 306 adolescents and young adults (14–24 y, 25 clinically depressed) using a multivariate statistical framework, based on canonical correlation analysis (CCA). By linking individual functional brain connectivity profiles to self-report questionnaires, IQ and demographic data we identified two distinct modes of covariation. The first mode mapped onto an externalization/internalization axis and showed a strong association with sex. The second mode mapped onto a well-being/distress axis independent of sex. Interestingly, both modes showed an association with age. Crucially, the changes in functional brain connectivity associated with changes in these phenotypes showed marked developmental effects. The findings point to a role for the default mode, frontoparietal and limbic networks in psychopathology and depression.
Early Cellular Responses of Prostate Carcinoma Cells to Sepantronium Bromide (YM155) Involve Suppression of mTORC1 by AMPK
Authors: Danielpour David , Gao Zhaofeng , Zmina Patrick M. , Shankar Eswar , Shultes Benjamin C. , Jobava Raul , Welford Scott M. , Hatzoglou Maria 
Published: August 2019

AbstractThe imidazolium compound YM155, first discovered as a potent inhibitor of Survivin, effectively kills many carcinomas in preclinical models. However, the upstream signaling mechanism triggered by YM155 remains unclear. Here we studied early signaling responses in vitro in prostate and renal cancer cell lines in a dose-dependent manner. We found that YM155 rapidly activates the retinoblastoma protein, correlating with the loss of expression of all three Cyclin Ds. Using Western blot, various selective chemical inhibitors and q-PCR, we show that YM155-mediated decrease in protein levels of Cyclin Ds, Survivin and Mcl-1 is independent of transcription or proteasomal control mechanisms. Moreover, we provide the first evidence that YM155 changes the phosphorylation status of known mTOR-target proteins involved in translational control, namely ribosomal protein S6 (rS6) and 4E-BP1. Our data support that YM155 achieves this by blocking mTORC1 via the phosphorylation of Raptor at S792 through activated AMPKα (T172). Furthermore, we also used a polysome profile, supporting that YM155 markedly suppresses cap-dependent translation of mRNAs which include Survivin, Cyclin D1 and Mcl-1. We provide the first evidence that YM155 functions as a potent activator of AMPKα, a robust suppressor of mTORC1 and an attenuator of global protein synthesis.
Human pressures on two estuaries of the Iberian Peninsula are reflected in food web structure
Authors: Donázar-Aramendía I. , Sánchez-Moyano J. E. , García-Asencio I. , Miró J. M. , Megina C. , García-Gómez J. C. 
Published: August 2019

AbstractAs a result of the increased urban and agricultural development in coastal environments, estuaries are among the most modified and threatened aquatic ecosystems. This study used stable isotopes to examine the effects of human impacts by contrasting the food web structures of two Iberian estuaries exposed to different degrees of human pressure. More complex feeding pathways were found in the more altered estuary (Guadalquivir). Greater spread among species along the carbon axis suggests that the primary consumers exploit organic matter with various origins, whereas different nitrogen signals of the secondary consumers suggest that they feed on different suites of prey. In contrast, the similar isotopic signals of secondary consumers in the relatively little influenced estuary (Guadiana) suggests similarity in diet composition and feeding on the same organic matter sources. Understanding trophic interactions in estuaries is vital for defining proper management and conservation, and the preliminary data provided here are one step in this direction.
ANO5 mutations in the Polish limb girdle muscular dystrophy patients: Effects on the protein structure
Authors: Jarmula Adam , Łusakowska Anna , Fichna Jakub P. , Topolewska Malgorzata , Macias Anna , Johnson Katherine , Töpf Ana , Straub Volker , Rosiak Edyta , Szczepaniak Krzysztof , Dunin-Horkawicz Stanisław , Maruszak Aleksandra , Kaminska Anna M. , Redowicz Maria Jolanta 
Published: August 2019

AbstractLGMD2L is a subtype of limb-girdle muscular dystrophy (LGMD), caused by recessive mutations in ANO5, encoding anoctamin-5 (ANO5). We present the analysis of five patients with skeletal muscle weakness for whom heterozygous mutations within ANO5 were identified by whole exome sequencing (WES). Patients varied in the age of the disease onset (from 22 to 38 years) and severity of the morphological and clinical phenotypes. Out of the nine detected mutations one was novel (missense p.Lys132Met, accompanied by p.His841Asp) and one was not yet characterized in the literature (nonsense, p.Trp401Ter, accompanied by p.Asp81Gly). The p.Asp81Gly mutation was also identified in another patient carrying a p.Arg758Cys mutation as well. Also, a c.191dupA frameshift (p.Asn64LysfsTer15), the first described and common mutation was identified. Mutations were predicted by in silico tools to have damaging effects and are likely pathogenic according to criteria of the American College of Medical Genetics and Genomics (ACMG). Indeed, molecular modeling of mutations revealed substantial changes in ANO5 conformation that could affect the protein structure and function. In addition, variants in other genes associated with muscle pathology were identified, possibly affecting the disease progress. The presented data indicate that the identified ANO5 mutations contribute to the observed muscle pathology and broaden the genetic spectrum of LGMD myopathies.
Ex vivo assessment of bicuspidization repair in treating severe functional tricuspid regurgitation: a stereo-scopic PIV study
Authors: Nguyen Yen Ngoc , Kabinejadian Foad , Ismail Munirah , Kong William Kok-Fai , Tay Edgar Lik Wui , Leo Hwa Liang 
Published: August 2019

AbstractThere has been a resurgence of interest in the treatment of severe functional tricuspid regurgitation (FTR) due to the awareness of its poor outcomes and potential percutaneous therapies. Kay bicuspidization has been adapted in percutaneous therapies but its clinical outcome remains uncertain. The present study evaluates the efficacy of Kay repair in a novel ex vivo pulsatile system. Porcine tricuspid valve (TV) (n = 3) was extracted and incorporated into a patient-specific silicon right ventricle (RV) emulating severe FTR, on which Kay repair was subsequently performed. TV area metrics and RV hemodynamic assessment by means of stereo-scopic particle image velocimetry were quantified in both FTR and post-repair conditions. Bicuspidization led to significant increase in cardiac output although the overall increment due to this approach alone was generally small, possibly due to existence of residual TR and the large reduction in TV opening area. Kinetic energy and viscous loss levels were increased post-repair, especially during diastolic filling. Main vortex structures generally maintained post-procedural. However, there was enhanced swirling motion in larger RV domain. Although this might reduce mural-thrombus risk, the relatively more complex vortex phenomenon likely resulted in elevated viscous loss observed and may potentially impact long-term adaptation. The RV hemodynamic alteration after tricuspid repair could be used to predict the success of these future transcatheter solutions.
A promising form-stable phase change material prepared using cost effective pinecone biochar as the matrix of palmitic acid for thermal energy storage
Authors: Wan Ye-chao , Chen Yan , Cui Zhi-xing , Ding Han , Gao Shu-feng , Han Zhi , Gao Jun-kai 
Published: August 2019

AbstractA promising new form-stable phase change material (PA/PB) was fabricated using pinecone biochar (PB) as the supporting material of palmitic acid (PA). The biochar of PB with large surface area was produced by forest residue of pinecone, and it was cheap, environment friendly and easy to prepare. The PB was firstly utilized as the supporter of PA and the characterizations of PA/PB were analyzed by the BET, SEM, XRD, DSC, TGA, FT-IR and thermal conductivity tester. The results demonstrated that the PA was physically absorbed by the PB and the crystal structure of the PA was not destroyed. The results of DSC showed that the fusing and crystallization points of the form-stable phase change material with the maximum content of PA (PA/PB-4) were 59.25 °C and 59.13 °C, and its fusing and freezing latent heat were 84.74 kJ/kg and 83.81 kJ/kg, respectively. The results of TGA suggested that the thermal stability of the PA/PB-4 composite was excellent, which could be used for the applications of thermal energy storage. Furthermore, the thermal conductivity of PA/PB-4 was 0.3926 W/(m∙K), which was increased by 43.76% compared with that of the pure PA. Thus, the study results indicated that the PA/PB-4 had great potential for thermal energy storage applications.
The droplet size of emulsion adjuvants has significant impact on their potency, due to differences in immune cell-recruitment and -activation
Authors: Shah Ruchi R. , Taccone Marianna , Monaci Elisabetta , Brito Luis A. , Bonci Alessandra , O’Hagan Derek T. , Amiji Mansoor M. , Seubert Anja 
Published: August 2019

AbstractSelf-emulsification is routinely used for oral delivery of lipophilic drugs in vivo, with the emulsion forming in vivo. We modified this technique to prepare novel oil-in-water emulsions of varying droplet size and composition on bench to enable adjuvanted vaccine delivery. We used these formulations to show that smaller droplets (20 nm) were much less effective as adjuvants for an influenza vaccine in mice than the emulsion droplet size of commercial influenza vaccine adjuvants (~160 nm). This was unexpected, given the many claims in the literature of the advantages of smaller particulates. We also undertook cell-recruitment mechanistic studies at site of injection and draining lymph nodes to directly address the question of why the smaller droplets were less effective. We discovered that emulsion droplet size and composition have a considerable impact on the ability to recruit immune cells to the injection site. We believe that further work is warranted to more extensively explore the question of whether, the smaller is not ‘better’, is a more common observation for particulate adjuvants.
Heart Rate Variability reveals the fight between racially biased and politically correct behaviour
Authors: Di Palma M. , Arcangeli E. , Lattanzi D. , Gabbiadini A. , Gallucci M. , Cuppini R. , Minelli A. , Berlingeri M. 
Published: August 2019

AbstractIn this study, we explored vagally-mediated heart rate variability (vmHRV) responses, a psychophysiological index of cognitive self-regulatory control, to map the dynamics associated with empathic responses for pain towards an out-group member. Accordingly, Caucasian participants were asked to judge the experience of African and Caucasian actors touched with either a neutral or a harmful stimulus. Results showed that (1) explicit judgment of pain intensity in African actors yielded higher rating score and (2) took longer time compared to Caucasian actors, (3) these behavioural outcomes were associated with a significant increment of RMSSD, Log-HF-HRV and HF-HRV n.u., (4) resting HF-HRV n.u. predicted the participants’ lag-time to judge painful stimulations delivered to African actors. Interestingly, these dynamics were associated with a measure of implicit racial attitudes and were, in part, abolished when participants performed a concurrent task during videos presentation. Taken together our results support the idea that a cognitive effort is needed to self-regulate our implicit attitude as predicted by the ‘Contrasting Forces Model’.
Polarization dependence of second harmonic generation from plasmonic nanoprism arrays
Authors: Raygoza-Sánchez K. Y. , Rocha-Mendoza I. , Segovia P. , Krasavin A. V. , Marino G. , Cesca T. , Michieli N. , Mattei G. , Zayats A. V. , Rangel-Rojo R. 
Published: August 2019

AbstractThe second order nonlinear optical response of gold nanoprisms arrays is investigated by means of second harmonic generation (SHG) experiments and simulations. The polarization dependence of the nonlinear response exhibits a 6-fold symmetry, attributed to the local field enhancement through the excitation of the surface plasmon resonances in bow-tie nanoantennas forming the arrays. Experiments show that for polarization of the input light producing excitation of the plasmonic resonances in the bow-tie nanoantennas, the SHG signal is enhanced; this despite the fact that the linear absorption spectrum is not dependent on polarization. The results are confirmed by electrodynamic simulations which demonstrate that SHG is also determined by the local field distribution in the nanoarrays. Moreover, the maximum of SHG intensity is observed at slightly off-resonance excitation, as implemented in the experiments, showing a close relation between the polarization dependence and the structure of the material, additionally revealing the importance of the presence of non-normal electric field components as under focused beam and oblique illumination.
Development of a viability digital PCR protocol for the selective detection and quantification of live Erwinia amylovora cells in cankers
Authors: Santander Ricardo D. , Meredith Christopher L. , Aćimović Srđan G. 
Published: August 2019

AbstractFire blight is a devastating disease of apple and pear caused by the bacterium Erwinia amylovora. One of its main symptoms is canker formation on perennial tissues which may lead to the death of limbs and/or the entire tree. E. amylovora overwinters in cankers which play an important role in initiating fire blight epidemics. However, knowledge of pathogen biology in cankers is scarce, in part due to limitations of classical microbiology methods and the inability of most molecular techniques to distinguish live from dead cells. In this work, a viability digital PCR (v-dPCR) protocol using propidium monoazide (PMA) was developed, allowing for the first time the selective detection and absolute quantification of E. amylovora live cells in apple and pear cankers collected in two time periods. Some key factors affecting the v-dPCR performance were the maceration buffer composition, the target DNA amplicon length, the thermal cycle number and the use of sodium dodecyl sulfate or PMA enhancer for Gram-negative bacteria to improve the effect of PMA. In the future, this methodology could shed light on E. amylovora population dynamics in cankers and provide clues on the effect of management practices, host cultivar, host water/nutritional status, etc., on bacterial survival.