bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new island-scale tropical cyclone outlook for southwest Pacific nations and territories
Authors: Magee Andrew D. , Lorrey Andrew M. , Kiem Anthony S. , Colyvas Kim 
Published: July 2020

AbstractThe southwest Pacific (SWP) region is vulnerable to tropical cyclone (TC) related impacts which adversely affect people, infrastructure and economies across several nations and territories. Skilful TC outlooks are needed for this region, but the erratic nature of SWP TCs and the complex ocean–atmosphere interactions that influence TC behaviour on seasonal timescales presents significant challenges. Here, we present a new TC outlook tool for the SWP using multivariate Poisson regression with indices of multiple climate modes. This approach provides skilful, island-scale TC count outlooks from July (four months ahead of the official TC season start in November). Monthly island-scale TC frequency outlooks are generated between July and December, enabling continuous refinement of predicted TC counts before and during a TC season. Use of this approach in conjunction with other seasonal climate guidance (including dynamical models) has implications for preparations ahead of severe weather events, resilience and risk reduction.
Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency
Authors: Mulholland Christopher B. , Traube Franziska R. , Ugur Enes , Parsa Edris , Eckl Eva-Maria , Schönung Maximilian , Modic Miha , Bartoschek Michael D. , Stolz Paul , Ryan Joel , Carell Thomas , Leonhardt Heinrich , Bultmann Sebastian 
Published: July 2020

AbstractCytosine DNA bases can be methylated by DNA methyltransferases and subsequently oxidized by TET proteins. The resulting 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) are considered demethylation intermediates as well as stable epigenetic marks. To dissect the contributions of these cytosine modifying enzymes, we generated combinations of Tet knockout (KO) embryonic stem cells (ESCs) and systematically measured protein and DNA modification levels at the transition from naive to primed pluripotency. Whereas the increase of genomic 5-methylcytosine (5mC) levels during exit from pluripotency correlated with an upregulation of the de novo DNA methyltransferases DNMT3A and DNMT3B, the subsequent oxidation steps turned out to be far more complex. The strong increase of oxidized cytosine bases (5hmC, 5fC, and 5caC) was accompanied by a drop in TET2 levels, yet the analysis of KO cells suggested that TET2 is responsible for most 5fC formation. The comparison of modified cytosine and enzyme levels in Tet KO cells revealed distinct and differentiation-dependent contributions of TET1 and TET2 to 5hmC and 5fC formation arguing against a processive mechanism of 5mC oxidation. The apparent independent steps of 5hmC and 5fC formation suggest yet to be identified mechanisms regulating TET activity that may constitute another layer of epigenetic regulation.
Evolutionary algorithms converge towards evolved biological photonic structures
Authors: Barry Mamadou Aliou , Berthier Vincent , Wilts Bodo D. , Cambourieux Marie-Claire , Bennet Pauline , Pollès Rémi , Teytaud Olivier , Centeno Emmanuel , Biais Nicolas , Moreau Antoine 
Published: July 2020

AbstractNature features a plethora of extraordinary photonic architectures that have been optimized through natural evolution in order to more efficiently reflect, absorb or scatter light. While numerical optimization is increasingly and successfully used in photonics, it has yet to replicate any of these complex naturally occurring structures. Using evolutionary algorithms inspired by natural evolution and performing particular optimizations (maximize reflection for a given wavelength, for a broad range of wavelength or maximize the scattering of light), we have retrieved the most stereotypical natural photonic structures. Whether those structures are Bragg mirrors, chirped dielectric mirrors or the gratings on top of Morpho butterfly wings, our results indicate how such regular structures might have spontaneously emerged in nature and to which precise optical or fabrication constraints they respond. Comparing algorithms show that recombination between individuals, inspired by sexual reproduction, confers a clear advantage that can be linked to the fact that photonic structures are fundamentally modular: each part of the structure has a role which can be understood almost independently from the rest. Such anin silicoevolution also suggests original and elegant solutions to practical problems, as illustrated by the design of counter-intuitive anti-reflective coatings for solar cells.
Computational analysis of androgen receptor (AR) variants to decipher the relationship between protein stability and related-diseases
Authors: Chen Fangfang , Chen Xiaoqing , Jiang Fan , Leng Feng , Liu Wei , Gui Yaoting , Yu Jing 
Published: July 2020

AbstractAlthough more than 1,000 androgen receptor (AR) mutations have been identified and these mutants are pathologically important, few theoretical studies have investigated the role of AR protein folding stability in disease and its relationship with the phenotype of the patients. Here, we extracted AR variant data from four databases: ARDB, HGMD, Cosmic, and 1,000 genome. 905 androgen insensitivity syndrome (AIS)-associated loss-of-function mutants and 168 prostate cancer-associated gain-of-function mutants in AR were found. We analyzed the effect of single-residue variation on the folding stability of AR by FoldX and guanidine hydrochloride denaturation experiment, and found that genetic disease-associated mutations tend to have a significantly greater effect on protein stability than gene polymorphisms. Moreover, AR mutants in complete androgen insensitivity syndrome (CAIS) tend to have a greater effect on protein stability than in partial androgen insensitive syndrome (PAIS). This study, by linking disease phenotypes to changes in AR stability, demonstrates the importance of protein stability in the pathogenesis of hereditary disease.
Vertical distribution of brittle star larvae in two contrasting coastal embayments: implications for larval transport
Authors: Guillam Morgane , Bessin Claire , Blanchet-Aurigny Aline , Cugier Philippe , Nicolle Amandine , Thiébaut Éric , Comtet Thierry 
Published: July 2020

AbstractThe ability of marine invertebrate larvae to control their vertical position shapes their dispersal pattern. In species characterized by large variations in population density, like many echinoderm species, larval dispersal may contribute to outbreak and die-off phenomena. A proliferation of the ophiuroidOphiocomina nigrawas observed for several years in western Brittany (France), inducing drastic changes on the benthic communities. We here studied the larval vertical distribution in this species and two co-occurring ophiuroid species,Ophiothrix fragilisandAmphiura filiformis, in two contrasting hydrodynamic environments: stratified in the bay of Douarnenez and well-mixed in the bay of Brest. Larvae were collected at 3 depths during 25 h within each bay. In the bay of Brest, all larvae were evenly distributed in the water column due to the intense vertical mixing. Conversely, in the bay of Douarnenez, a diel vertical migration was observed forO. nigra, with a night ascent of young larvae, and ontogenetic differences.These different patterns in the two bays mediate the effects of tidal currents on larval fluxes.O. fragilislarvae were mainly distributed above the thermocline which may favour larval retention within the bay, whileA. filiformislarvae, mostly concentrated near the bottom, were preferentially exported. This study highlighted the complex interactions between coastal hydrodynamics and specific larval traits, e.g. larval morphology, in the control of larval vertical distribution and larval dispersal.
A fully sustainable, self-poled, bio-waste based piezoelectric nanogenerator: electricity generation from pomelo fruit membrane
Authors: Bairagi Satyaranjan , Ghosh Saikat , Ali S. Wazed 
Published: July 2020

AbstractA self-powered system is very much essential aspect in the recent trend to improve the working efficiency of the portable and wearable devices. Here, we have reported a fully sustainable, self-poled, bio-compatible, and bio-waste based piezoelectric energy harvester which has been made of Pomelo Fruit Membrane (PFM). PFM based piezoelectric generator (PFMBPEG) could generate ~ 6.4 V output voltage and ~ 7.44 μA output current directly, only by finger tapping on the device and registers a power density of ~ 12 μW cm−2 whereas, the same piezoelectric generator can generate ~ 15 V output voltage, 130 μA output current, and power density of ~ 487.5 μW cm−2 by using a full wave rectifier. The sensitivity and energy harvesting competence of the generator have also been assessed by attaching this nanogenerator into various parts of human body (as energy sources) such as wrist, elbow, finger, throat, jaws, leg and putting the device into ultrasonic bath and in every case, it could successfully generate voltage. Therefore, this bio-waste based energy harvester can be used as a power source for the different potable and wearable electronic goods where a small amount of energy is required, specifically in the biomedical applications (i.e., health monitoring, power source for the implantable devices and so on). Finally, mechanical stability the developed piezoelectric generator has been evaluated by cyclic bending test and it has been observed that there is no significant deformation of the PFM film even after 100 cycles.
Real-time metabolic profiling of oesophageal tumours reveals an altered metabolic phenotype to different oxygen tensions and to treatment with Pyrazinib
Authors: Buckley Amy M. , Dunne Margaret R. , Morrissey Maria E. , Kennedy Susan A. , Nolan Aoife , Davern Maria , Foley Emma K. , Clarke Niamh , Lysaght Joanne , Ravi Narayanasamy , O’Toole Dermot , MacCarthy Finbar , Reynolds John V. , Kennedy Breandán N. , O’Sullivan Jacintha 
Published: July 2020

AbstractOesophageal cancer is the 6th most common cause of cancer related death worldwide. The current standard of care for oesophageal adenocarcinoma (OAC) focuses on neoadjuvant therapy with chemoradiation or chemotherapy, however the 5-year survival rates remain at < 20%. To improve treatment outcomes it is critical to further investigate OAC tumour biology, metabolic phenotype and their metabolic adaptation to different oxygen tensions. In this study, by using human ex-vivo explants we demonstrated using real-time metabolic profiling that OAC tumour biopsies have a significantly higher oxygen consumption rate (OCR), a measure of oxidative phosphorylation compared to extracellular acidification rate (ECAR), a measure of glycolysis (p = 0.0004). Previously, we identified a small molecule compound, pyrazinib which enhanced radiosensitivity in OAC. Pyrazinib significantly inhibited OCR in OAC treatment-naïve biopsies (p = 0.0139). Furthermore, OAC biopsies can significantly adapt their metabolic rate in real-time to their environment. Under hypoxic conditions pyrazinib produced a significant reduction in both OCR (p = 0.0313) and ECAR in OAC treatment-naïve biopsies. The inflammatory secretome profile from OAC treatment-naïve biopsies is heterogeneous. OCR was positively correlated with three secreted factors in the tumour conditioned media: vascular endothelial factor A (VEGF-A), IL-1RA and thymic stromal lymphopoietin (TSLP). Pyrazinib significantly inhibited IL-1β secretion (p = 0.0377) and increased IL-3 (p = 0.0020) and IL-17B (p = 0.0181). Importantly, pyrazinib did not directly alter the expression of dendritic cell maturation markers or reduce T-cell viability or activation markers. We present a new method for profiling the metabolic rate of tumour biopsies in real-time and demonstrate the novel anti-metabolic and anti-inflammatory action of pyrazinib ex-vivo in OAC tumours, supporting previous findings in-vitro whereby pyrazinib significantly enhanced radiosensitivity in OAC.
Early evidence of fire in south-western Europe: the Acheulean site of Gruta da Aroeira (Torres Novas, Portugal)
Authors: Sanz Montserrat , Daura Joan , Cabanes Dan , Égüez Natalia , Carrancho Ángel , Badal Ernestina , Souto Pedro , Rodrigues Filipa , Zilhão João 
Published: July 2020

AbstractThe site of Gruta da Aroeira (Torres Novas, Portugal), with evidence of human occupancy dating to ca. 400 ka (Marine Isotope Stage 11), is one of the very few Middle Pleistocene localities to have provided a fossil hominin cranium associated with Acheulean bifaces in a cave context. The multi-analytic study reported here of the by-products of burning recorded in layer X suggests the presence of anthropogenic fires at the site, among the oldest such evidence in south-western Europe. The burnt material consists of bone, charcoal and, possibly, quartzite cobbles. These finds were made in a small area of the cave and in two separate occupation horizons. Our results add to our still-limited knowledge about the controlled use of fire in the Lower Palaeolithic and contribute to ongoing debates on the behavioural complexity of the Acheulean of Europe.
Blockade of the TLR4–MD2 complex lowers blood pressure and improves vascular function in a murine model of type 1 diabetes
Authors: de Oliveira Amanda Almeida , Faustino Josemar , Webb R. Clinton , Nunes Kenia Pedrosa 
Published: July 2020

AbstractWhile the pathogenesis of diabetes-induced high blood pressure (BP) is not entirely clear, current evidence suggests that Toll-like receptor 4 (TLR4) is a key player in the mechanisms associated with hypertension. However, it is unknown whether this receptor affects BP under type 1 diabetes. Likewise, there is insufficient knowledge about the role of TLR4 in diabetes-associated vascular dysfunction of large arteries. To narrow these gaps, in this study, we investigated if blockade of the TLR4-MD2 complex impacts BP and vascular function in diabetic rats. We injected streptozotocin in male Sprague Dawley rats and treated them with a neutralizing anti-TLR4 antibody for 14 days. BP was directly measured in conscious animals at the end of the treatment. In another set of experiments, we excised the aorta from control and diabetic animals, and measured TLR4 and MD2—a co-receptor that confers functionality to TLR4—levels by Western blotting. We also performed functional studies and evaluated ROS levels with and without a pharmacological inhibitor for TLR4 as well as for MD2. Additionally, we scrutinized a large human RNA-Seq dataset of aortic tissue to assess the co-expression of TLR4, MD2, and subunits of the vascular NADPH oxidases under diabetes and hypertension. We report that (a) chronic blockade of the TLR4–MD2 complex lowers BP in diabetic animals; that (b) type 1 diabetes modulates the levels of MD2 expression in the aorta, but not TLR4, at least in the conditions evaluated in this study; and, that (c) acute inhibition of TLR4 or MD2 diminishes vascular contractility and reduces oxidative stress in the aorta of these animals. In summary, we show evidence that the TLR4–MD2 complex is involved in the mechanisms linking type 1 diabetes and hypertension.
Numerical and analytical results for geometric measure of coherence and geometric measure of entanglement
Authors: Zhang Zhou , Dai Yue , Dong Yu-Li , Zhang Chengjie 
Published: July 2020

AbstractQuantifying coherence and entanglement is extremely important in quantum information processing. Here, we present numerical and analytical results for the geometric measure of coherence, and also present numerical results for the geometric measure of entanglement. On the one hand, we first provide a semidefinite algorithm to numerically calculate geometric measure of coherence for arbitrary finite-dimensional mixed states. Based on this semidefinite algorithm, we test randomly generated single-qubit states, single-qutrit states, and a special kind of d-dimensional mixed states. Moreover, we also obtain an analytical solution of geometric measure of coherence for a special kind of mixed states. On the other hand, another algorithm is proposed to calculate the geometric measure of entanglement for arbitrary two-qubit and qubit-qutrit states, and some special kinds of higher dimensional mixed states. For other states, the algorithm can get a lower bound of the geometric measure of entanglement. Randomly generated two-qubit states, the isotropic states and the Werner states are tested. Furthermore, we compare our numerical results with some analytical results, which coincide with each other.
The emergence and adaptive use of prestige in an online social learning task
Authors: Brand C. O. , Heap S. , Morgan T. J. H. , Mesoudi A. 
Published: July 2020

AbstractPrestige-biased social learning occurs when individuals preferentially learn from others who are highly respected, admired, copied, or attended to in their group. This form of social learning is argued to reflect novel forms of social hierarchy in human societies, and, by providing an efficient short-cut to acquiring adaptive information, underpin the cumulative cultural evolution that has contributed to our species’ ecological success. Despite these potentially important consequences, little empirical work to date has tested the basic predictions of prestige-biased social learning. Here we provide evidence supporting the key predictions that prestige-biased social learning is used when it constitutes an indirect cue of success, and when success-biased social learning is unavailable. We ran an online experiment (n = 269) in which participants could copy each other in real-time to score points on a general-knowledge quiz. Our implementation of ‘prestige’ was the number of times someone had previously been copied by others. Importantly, prestige was an emergent property of participants’ behaviour during the experiment; no deception or manipulation of prestige was employed at any time. We found that, as predicted, participants used prestige-biased social learning when the prestige cue was an indirect cue of success, and when direct success information was unavailable. This highlights how people flexibly and adaptively employ social learning strategies based on the reliability of the information that such strategies provide.
Gold nanoparticle mediated radiation response among key cell components of the tumour microenvironment for the advancement of cancer nanotechnology
Authors: Bromma Kyle , Cicon Leah , Beckham Wayne , Chithrani Devika B. 
Published: July 2020

AbstractOne of the major issues in cancer radiotherapy (RT) is normal tissue toxicity. Introduction of radiosensitizers like gold nanoparticles (GNPs) into cancer cells to enhance the local RT dose has been tested successfully. However, it is not known how GNPs interact with other stromal cells such as normal fibroblasts (FBs) and cancer associated fibroblasts (CAFs) within the tumour microenvironment. It is known that FBs turn into CAFs to promote tumour growth. Hence, we used FBs and CAFs along with HeLa (our cancer cell line) to evaluate the differences in GNP uptake and resulting radiation induced damage to elucidate the GNP-mediated therapeutic effect in RT. The CAFs had the largest uptake of the GNPs per cell, with on average 265% relative to HeLa while FBs had only 7.55% the uptake of HeLa and 2.87% the uptake of CAFs. This translated to increases in 53BP1-related DNA damage foci in CAFs (13.5%) and HeLa (9.8%) compared to FBs (8.8%) with RT treatment. This difference in DNA damage due to selective targeting of cancer associated cells over normal cells may allow GNPs to be an effective tool in future cancer RT to battle normal tissue toxicity while improving local RT dose to the tumour.
IL-10 attenuates OxPCs-mediated lipid metabolic responses in ischemia reperfusion injury
Authors: Bagchi Ashim K. , Surendran Arun , Malik Akshi , Jassal Davinder S. , Ravandi Amir , Singal Pawan K. 
Published: July 2020

AbstractOxidized phospholipids (OxPLs) promote inflammation as well as low density lipoprotein (LDL) uptake in a variety of physiological and pathological states. Given the anti-inflammatory role of the cytokine IL-10, we investigated its modulatory effect on the production of oxidized phosphatidylcholines (OxPCs) as well as lipid metabolic responses in global myocardial ischemia/reperfusion (I/R) injury. Increased OxPCs levels, by 1-Palmitoyl-2-(5-oxovaleryl)-sn-glycero-3-phosphocholine (POVPC), promoted oxidative stress (OS) and cell death. OxPCs-mediated-OS, resulted in oxidized low-density lipoprotein receptor 1 (LOX-1) activation and upregulated the expression of toll-like receptor 2 (TLR2). IL-10-induced increase in proprotein convertase subtilisin/kexin type 9 (PCSK9) negatively regulated LOX-1 as well as TLR2 inflammatory responses. Under stress conditions, phosphorylation of sterol regulatory element binding protein 1c (SREBP 1c) was prevented by IL-10. The latter also prevented the generation of OxPCs and reduced their ratio (OxPCs/PCs) during injury. LOX-1 activation also promoted SREBP1c-mediated TGF-βRII expression which was inhibited by IL-10. Both fragmented and non-fragmented OxPCs were elevated during I/R and this effect was attenuated by IL-10. The largest impact (two–threefold change at log2) was on PAzPC, (1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine)—a fragmented OxPC. Thus it appears that among different OxPCs, IL-10 significantly reduces a single molecule (PAzPC)-mediated lipid metabolic responses in cardiomyocytes thereby mitigating inflammation and cell death.
Cancer cells grown in 3D under fluid flow exhibit an aggressive phenotype and reduced responsiveness to the anti-cancer treatment doxorubicin
Authors: Azimi Tayebeh , Loizidou Marilena , Dwek Miriam V. 
Published: July 2020

Abstract3D laboratory models of cancer are designed to recapitulate the biochemical and biophysical characteristics of the tumour microenvironment and aim to enable studies of cancer, and new therapeutic modalities, in a physiologically-relevant manner. We have developed an in vitro 3D model comprising a central high-density mass of breast cancer cells surrounded by collagen type-1 and we incorporated fluid flow and pressure. We noted significant changes in cancer cell behaviour using this system. MDA-MB231 and SKBR3 breast cancer cells grown in 3D downregulated the proliferative marker Ki67 (P < 0.05) and exhibited decreased response to the chemotherapeutic agent doxorubicin (DOX) (P < 0.01). Mesenchymal markers snail and MMP14 were upregulated in cancer cells maintained in 3D (P < 0.001), cadherin-11 was downregulated (P < 0.001) and HER2 increased (P < 0.05). Cells maintained in 3D under fluid flow exhibited a further reduction in response to DOX (P < 0.05); HER2 and Ki67 levels were also attenuated. Fluid flow and pressure was associated with reduced cell viability and decreased expression levels of vimentin. In summary, aggressive cancer cell behaviour and reduced drug responsiveness was observed when breast cancer cells were maintained in 3D under fluid flow and pressure. These observations are relevant for future developments of 3D in vitro cancer models and organ-on-a-chip initiatives.