bluuebunny/crossref_metadata_2025 huggingface dataset:
Animal invaders threaten protected areas worldwide
Authors: Liu Xuan , Blackburn Tim M. , Song Tianjian , Wang Xuyu , Huang Cong , Li Yiming
Published: June 2020

Protected areas are the cornerstone of biodiversity conservation. However, alien species invasion is an increasing threat to biodiversity, and the extent to which protected areas worldwide are resistant to incursions of alien species remains poorly understood. Here, we investigate establishment by 894 terrestrial alien animals from 11 taxonomic groups including vertebrates and invertebrates across 199,957 protected areas at the global scale. We find that <10% of protected areas are home to any of the alien animals, but there is at least one established population within 10-100 km of the boundaries of 89%-99% of protected areas, while >95% of protected areas are environmentally suitable for establishment. Higher alien richness is observed in IUCN category-II national parks supposedly with stricter protection, and in larger protected areas with higher human footprint and more recent designation. Our results demonstrate that protected areas provide important protection from biological invasions, but invasions may become an increasingly dominant problem in the near future.
Perceptions of childhood asthma and its control among Malays in Malaysia: a qualitative study
Authors: Sukri Nursyuhada , Ramdzan Siti Nurkamilla , Liew Su May , Salim Hani , Khoo Ee Ming
Published: June 2020

Children with poor asthma control have poor health outcomes. In Malaysia, the Malays have the highest asthma prevalence and poorest control compared to other ethnicities. We aimed to explore Malay children with asthma and their parents’ perceptions on asthma and its control. We conducted focus group discussions (FGD) using a semi-structured interview guide. Interviews were audio-recorded, transcribed verbatim and analysed thematically. Sixteen children and parents (N = 32) participated. The perception of asthma was based on personal experience, cultural and religious beliefs, and there was mismatch between children and parents. Parents perceived mild symptoms as normal, some had poor practices, raising safety concerns as children were dependent on them for self-management. Conflicting religious opinions on inhaler use during Ramadhan caused confusion in practice. Parents perceived a lack of system support towards asthma care and asthma affected quality of life. Urgent intervention is needed to address misconceptions to improve asthma care in children.
Roadmap for naming uncultivated Archaea and Bacteria
Authors: Murray Alison E. , Freudenstein John , Gribaldo Simonetta , Hatzenpichler Roland , Hugenholtz Philip , Kämpfer Peter , Konstantinidis Konstantinos T. , Lane Christopher E. , Papke R. Thane , Parks Donovan H. , Rossello-Mora Ramon , Stott Matthew B. , Sutcliffe Iain C. , Thrash J. Cameron , Venter Stephanus N. , Whitman William B. , Acinas Silvia G. , Amann Rudolf I. , Anantharaman Karthik , Armengaud Jean , Baker Brett J. , Barco Roman A. , Bode Helge B. , Boyd Eric S. , Brady Carrie L. , Carini Paul , Chain Patrick S. G. , Colman Daniel R. , DeAngelis Kristen M. , de los Rios Maria Asuncion , Estrada-de los Santos Paulina , Dunlap Christopher A. , Eisen Jonathan A. , Emerson David , Ettema Thijs J. G. , Eveillard Damien , Girguis Peter R. , Hentschel Ute , Hollibaugh James T. , Hug Laura A. , Inskeep William P. , Ivanova Elena P. , Klenk Hans-Peter , Li Wen-Jun , Lloyd Karen G. , Löffler Frank E. , Makhalanyane Thulani P. , Moser Duane P. , Nunoura Takuro , Palmer Marike , Parro Victor , Pedrós-Alió Carlos , Probst Alexander J. , Smits Theo H. M. , Steen Andrew D. , Steenkamp Emma T. , Spang Anja , Stewart Frank J. , Tiedje James M. , Vandamme Peter , Wagner Michael , Wang Feng-Ping , Yarza Pablo , Hedlund Brian P. , Reysenbach Anna-Louise
Published: June 2020

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.
Interface Engineered Binary Platinum Free Alloy-based Counter Electrodes with Improved Performance in Dye-Sensitized Solar Cells
Authors: Liu Wen-Wu , Jiang Wei , Liu Yu-Cheng , Niu Wen-Jun , Liu Mao-Cheng , Kong Ling-Bin , Lee Ling , Wang Zhiming M. , Chueh Yu-Lun
Published: June 2020

The high cost and platinum dissolution issues of counter electrodes (CEs) are two core problems for the development of dye-sensitized solar cells (DSSCs). In this work, different CEs based on binary alloy Ru81.09Co18.91, Ru80.55Se19.45 and Co20.85Se79.15 nanostructures for DSSCs were successfully synthesized and investigated by a facile and environmentally friendly approach. Here, we found that the Co20.85Se79.15 alloy CE-based device yields the higher photoelectric conversion efficiency of 7.08% compared with that (5.80%) of the DSSC using a pure Pt CE because of the larger number of active sites with improved charge transferability and reduced interface resistance by matching work function with the I3‒/I‒ redox electrolyte. The inexpensive synthesis method, cost-effectiveness and superior catalytic activity of the Co20.85Se79.15 alloy may open up a new avenue for the development of CEs for DSSCs in the near future.
Resprouting trees drive understory vegetation dynamics following logging in a temperate forest
Authors: Matula Radim , Řepka Radomír , Šebesta Jan , Pettit Joseph L. , Chamagne Juliette , Šrámek Martin , Horgan Katherine , Maděra Petr
Published: June 2020

Removal of canopy trees by logging causes shifts in herbaceous diversity and increases invasibility of the forest understory. However, disturbed (cut) trees of many species do not die but resprout from remaining parts. Because sprouts develop vigorously immediately after disturbances, we hypothesized that sprouts of logged trees offset the changes in species richness and invasibility of the herbaceous layer by eliminating the rise in the resource availability during the time before regeneration from seeds develops. To test this, we analyzed data on herbaceous vegetation and sprout biomass collected in a broadleaved temperate forest in the Czech Republic before and for 6 years after logging. Sprouts that were produced by most of the stumps of logged trees offset large rises in species richness and cover of herbaceous plants and the resource availability that followed logging, but they affected the alien plants more significantly than the native plants. The sprouting canopy effectually eliminated most of the alien species that colonized the forest following a logging event. These findings indicate that in forests dominated by tree species with resprouting ability, sprouts drive the early post-disturbance dynamics of the herbaceous layer. By offsetting the post-disturbance vegetation shifts, resprouting supports forest resilience.
On Improving The Computing Capacity of Dynamical Systems
Authors: Athanasiou Vasileios , Konkoli Zoran
Published: June 2020

Reservoir Computing has emerged as a practical approach for solving temporal pattern recognition problems. The procedure of preparing the system for pattern recognition is simple, provided that the dynamical system (reservoir) used for computation is complex enough. However, to achieve a sufficient reservoir complexity, one has to use many interacting elements. We propose a novel method to reduce the number of reservoir elements without reducing the computing capacity of the device. It is shown that if an auxiliary input channel can be engineered, the drive, advantageous correlations between the signal one wishes to analyse and the state of the reservoir can emerge, increasing the intelligence of the system. The method has been illustrated on the problem of electrocardiogram (ECG) signal classification. By using a reservoir with only one element, and an optimised drive, more than 93% of the signals have been correctly labelled.
Introducing an Optimization- and explicit Runge-Kutta- based Approach to Perform Dynamic Flux Balance Analysis
Authors: Schroeder Wheaton L. , Saha Rajib
Published: June 2020

In this work we introduce the generalizedOptimization- and explicitRunge-Kutta-basedApproach (ORKA) to performdynamicFluxBalanceAnalysis (dFBA), which is numerically more accurate and computationally tractable than existing approaches. ORKA is applied to a four-tissue (leaf, root, seed, and stem) model ofArabidopsis thaliana, p-ath773, uniquely capturing the core-metabolism of several stages of growth from seedling to senescence at hourly intervals. Model p-ath773 has been designed to show broad agreement with published plant-scale properties such as mass, maintenance, and senescence, yet leaving reaction-level behavior unconstrainted. Hence, it serves as a framework to study the reaction-level behavior necessary for observed plant-scale behavior. Two such case studies of reaction-level behavior include the lifecycle progression of sulfur metabolism and the diurnal flow of water throughout the plant. Specifically, p-ath773 shows how transpiration drives water flow through the plant and how water produced by leaf tissue metabolism may contribute significantly to transpired water. Investigation of sulfur metabolism elucidates frequent cross-compartment exchange of a standing pool of amino acids which is used to regulate the proton flow. Overall, p-ath773 and ORKA serve as scaffolds for dFBA-based lifecycle modeling of plants and other systems to further broaden the scope ofin silicometabolic investigation.
Vestibular stimulation by 2G hypergravity modifies resynchronization in temperature rhythm in rats
Authors: Martin Tristan , Bonargent Tristan , Besnard Stéphane , Quarck Gaëlle , Mauvieux Benoit , Pigeon Eric , Denise Pierre , Davenne Damien
Published: June 2020

Input from the light/dark (LD) cycle constitutes the primary synchronizing stimulus for the suprachiasmatic nucleus (SCN) circadian clock. However, the SCN can also be synchronized by non-photic inputs. Here, we hypothesized that the vestibular system, which detects head motion and orientation relative to gravity, may provide sensory inputs to synchronize circadian rhythmicity. We investigated the resynchronization of core temperature (Tc) circadian rhythm to a six-hour phase advance of the LD cycle (LD + 6) using hypergravity (2 G) as a vestibular stimulation in control and bilateral vestibular loss (BVL) rats. Three conditions were tested: an LD + 6 exposure alone, a series of seven 2 G pulses without LD + 6, and a series of seven one-hour 2 G pulses (once a day) following LD + 6. First, following LD + 6, sham rats exposed to 2 G pulses resynchronized earlier than BVL rats (p = 0.01), and earlier than sham rats exposed to LD + 6 alone (p = 0.002). Each 2 G pulse caused an acute drop of Tc in sham rats (−2.8 ± 0.3 °C; p < 0.001), while BVL rats remained unaffected. This confirms that the vestibular system influences chronobiological regulation and supports the hypothesis that vestibular input, like physical activity, should be considered as a potent time cue for biological rhythm synchronization, acting in synergy with the visual system.
Potential Utilisation of Dark-Fermented Palm Oil Mill Effluent in Continuous Production of Biomethane by Self-Granulated Mixed Culture
Authors: Mahmod Safa Senan , Azahar Azratul Madihah , Luthfi Abdullah Amru Indera , Abdul Peer Mohamed , Mastar Mohd Shahbudin , Anuar Nurina , Takriff Mohd Sobri , Jahim Jamaliah M. D.
Published: June 2020

Two-stage anaerobic digestion of palm oil mill effluent (POME) is a promising method for converting the waste from the largest agricultural industry in Southeast Asia into a clean and sustainable energy. This study investigates the degradation of acid-rich effluent from the dark fermentation stage for the production of biomethane (BioCH4) in a 30-L continuous stirred-tank reactor (CSTR). The continuous methanogenic process was operated with varied HRTs (10 - 1 day) and OLRs (4.6–40.6 gCOD/L.d−1) under thermophilic conditions. Methanothermobacter sp. was the dominant thermophilic archaea that was responsible for the production rate of 4.3 LCH4/LPOME.d−1 and methane yield of 256.77 LCH4kgCOD at HRT of 2 d, which is the lowest HRT reported in the literature. The process was able to digest 85% and 64% of the initial POME’s COD and TSS, respectively. The formation of methane producing granules (MPG) played a pivotal role in sustaining the efficient and productive anaerobic system. We report herein that the anaerobic digestion was not only beneficial in reducing the contaminants in the liquid effluent, but generating BioCH4 gas with a positive net energy gain of 7.6 kJ/gCOD.
Flexible endoscopic micro-optical coherence tomography for three-dimensional imaging of the arterial microstructure
Authors: Kim Junyoung , Kim Sunwon , Song Joon Woo , Kim Hyun Jung , Lee Min Woo , Han Jeongmoo , Kim Jin Won , Yoo Hongki
Published: June 2020

Micro-optical coherence tomography (µOCT) is a novel imaging approach enabling visualization of the microstructures of biological tissues at a cellular or sub-cellular level. However, it has been challenging to develop a miniaturized flexible endoscopic µOCT probe allowing helical luminal scanning. In this study, we built a flexible endoscopic µOCT probe with an outer diameter of 1.2 mm, which acquires three-dimensional images of the arterial microstructures via helical scanning with an axial and lateral resolutions of 1.83 µm and 3.38 µm in air, respectively. Furthermore, the depth of focus of the µOCT imaging probe was extended two-fold using a binary phase spatial filter. We demonstrated that the present endoscopic µOCT could image cellular level features of a rabbit artery with high-risk atheroma and a bioresorbable scaffold-implanted swine coronary artery. This highly-translatable endoscopic µOCT will be a useful tool for investigating coronary artery disease and stent biology.
Cellular absorption of small molecules: free energy landscapes of melatonin binding at phospholipid membranes
Authors: Lu Huixia , Marti Jordi
Published: June 2020

Free energy calculations are essential to unveil mechanisms at the atomic scale such as binding of small solutes and their translocation across cell membranes, eventually producing cellular absorption. Melatonin regulates biological rhythms and is directly related to carcinogenesis and neurodegenerative disorders. Free energy landscapes obtained from well-tempered metadynamics simulations precisely describe the characteristics of melatonin binding to specific sites in the membrane and reveal the role of cholesterol in free energy barrier crossing. A specific molecular torsional angle and the distance between melatonin and the center of the membrane along the normal to the membrane Z-axis have been considered as suitable reaction coordinates. Free energy barriers between two particular orientations of the molecular structure (folded and extended) have been found to be of about 18 kJ/mol for z-distances of about 1–2 nm. The ability of cholesterol to expel melatonin out of the internal regions of the membrane towards the interface and the external solvent is explained from a free energy perspective. The calculations reported here offer detailed free energy landscapes of melatonin embedded in model cell membranes and reveal microscopic information on its transition between free energy minima, including the location of relevant transition states, and provide clues on the role of cholesterol in the cellular absorption of small molecules.
Enhanced tenacity of mycobacterial aerosols from necrotic neutrophils
Authors: Pfrommer E. , Dreier C. , Gabriel G. , Dallenga T. , Reimer R. , Schepanski K. , Scherließ R. , Schaible U. E. , Gutsmann T.
Published: June 2020

The tuberculosis agent Mycobacterium tuberculosis is primarily transmitted through air, but little is known about the tenacity of mycobacterium-containing aerosols derived from either suspensions or infected neutrophils. Analysis of mycobacterial aerosol particles generated from bacterial suspensions revealed an average aerodynamic diameter and mass density that may allow distant airborne transmission. The volume and mass of mycobacterial aerosol particles increased with elevated relative humidity. To more closely mimic aerosol formation that occurs in active TB patients, aerosols from mycobacterium-infected neutrophils were analysed. Mycobacterium-infected intact neutrophils showed a smaller particle size distribution and lower viability than free mycobacteria. In contrast, mycobacterium-infected necrotic neutrophils, predominant in M. tuberculosis infection, revealed particle sizes and viability rates similar to those found for free mycobacteria, but in addition, larger aggregates of viable mycobacteria were observed. Therefore, mycobacteria are shielded from environmental stresses in multibacillary aggregates generated from necrotic neutrophils, which allows improved tenacity but emphasizes short distance transmission between close contacts.
A heritable profile of six miRNAs in autistic patients and mouse models
Authors: Ozkul Yusuf , Taheri Serpil , Bayram Kezban Korkmaz , Sener Elif Funda , Mehmetbeyoglu Ecmel , Öztop Didem Behice , Aybuga Fatma , Tufan Esra , Bayram Arslan , Dolu Nazan , Zararsiz Gokmen , Kianmehr Leila , Beyaz Feyzullah , Doganyigit Züleyha , Cuzin François , Rassoulzadegan Minoo
Published: June 2020

Autism spectrum disorder (ASD) is a group of developmental pathologies that impair social communication and cause repetitive behaviors. The suggested roles of noncoding RNAs in pathology led us to perform a comparative analysis of the microRNAs expressed in the serum of human ASD patients. The analysis of a cohort of 45 children with ASD revealed that six microRNAs (miR-19a-3p, miR-361-5p, miR-3613-3p, miR-150-5p, miR-126-3p, and miR-499a-5p) were expressed at low to very low levels compared to those in healthy controls. A similar but less pronounced decrease was registered in the clinically unaffected parents of the sick children and in their siblings but never in any genetically unrelated control. Results consistent with these observations were obtained in the blood, hypothalamus and sperm of two of the established mouse models of ASD: valproic acid-treated animals and Cc2d1a+/− heterozygotes. In both instances, the same characteristic miRNA profile was evidenced in the affected individuals and inherited together with disease symptoms in the progeny of crosses with healthy animals. The consistent association of these genetic regulatory changes with the disease provides a starting point for evaluating the changes in the activity of the target genes and, thus, the underlying mechanism(s). From the applied societal and medical perspectives, once properly confirmed in large cohorts, these observations provide tools for the very early identification of affected children and progenitors.
Ensilicated tetanus antigen retains immunogenicity: in vivo study and time-resolved SAXS characterization
Authors: Doekhie A. , Dattani R. , Chen Y-C. , Yang Y. , Smith A. , Silve A. P. , Koumanov F. , Wells S. A. , Edler K. J. , Marchbank K. J. , Elsen J. M. H. van den , Sartbaeva A.
Published: June 2020

Our recently developed ensilication approach can physically stabilize proteins in silica without use of a pre-formed particle matrix. Stabilisation is done by tailor fitting individual proteins with a silica coat using a modified sol-gel process. Biopharmaceuticals, e.g. liquid-formulated vaccines with adjuvants, frequently have poor thermal stability; heating and/or freezing impairs their potency. As a result, there is an increase in the prevalence of vaccine-preventable diseases in low-income countries even when there are means to combat them. One of the root causes lies in the problematic vaccine ‘cold chain’ distribution. We believe that ensilication can improve vaccine availability by enabling transportation without refrigeration. Here, we show that ensilication stabilizes tetanus toxin C fragment (TTCF), a component of the tetanus toxoid present in the diphtheria, tetanus and pertussis (DTP) vaccine. Experimentalin vivoimmunization data show that the ensilicated material can be stored, transported at ambient temperatures, and even heat-treated without compromising the immunogenic properties of TTCF. To further our understanding of the ensilication process and its protective effect on proteins, we have also studied the formation of TTCF-silica nanoparticles via time-resolved Small Angle X-ray Scattering (SAXS). Our results reveal ensilication to be a staged diffusion-limited cluster aggregation (DLCA) type reaction. An early stage (tens of seconds) in which individual proteins are coated with silica is followed by a subsequent stage (several minutes) in which the protein-containing silica nanoparticles aggregate into larger clusters. Our results suggest that we could utilize this technology for vaccines, therapeutics or other biopharmaceuticals that are not compatible with lyophilization.
The effect of phytoglobin overexpression on the plant proteome during nonhost response of barley (Hordeum vulgare) to wheat powdery mildew (Blumeria graminis f. sp. tritici)
Authors: Andrzejczak O. A. , Sørensen C. K. , Wang W.-Q. , Kovalchuk S. , Hagensen C. E. , Jensen O. N. , Carciofi M. , Hovmøller M. S. , Rogowska-Wrzesinska A. , Møller I. M. , Hebelstrup K. H.
Published: June 2020

Nonhost resistance, a resistance of plant species against all nonadapted pathogens, is considered the most durable and efficient immune system in plants. To increase our understanding of the response of barley plants to infection by powdery mildew, Blumeria graminis f. sp. tritici, we used quantitative proteomic analysis (LC-MS/MS). We compared the response of two genotypes of barley cultivar Golden Promise, wild type (WT) and plants with overexpression of phytoglobin (previously hemoglobin) class 1 (HO), which has previously been shown to significantly weaken nonhost resistance. A total of 8804 proteins were identified and quantified, out of which the abundance of 1044 proteins changed significantly in at least one of the four comparisons (‘i’ stands for ‘inoculated’)- HO/WT and HOi/WTi (giving genotype differences), and WTi/WT and HOi/HO (giving treatment differences). Among these differentially abundant proteins (DAP) were proteins related to structural organization, disease/defense, metabolism, transporters, signal transduction and protein synthesis. We demonstrate that quantitative changes in the proteome can explain physiological changes observed during the infection process such as progression of the mildew infection in HO plants that was correlated with changes in proteins taking part in papillae formation and preinvasion resistance. Overexpression of phytoglobins led to modification in signal transduction prominently by dramatically reducing the number of kinases induced, but also in the turnover of other signaling molecules such as phytohormones, polyamines and Ca2+. Thus, quantitative proteomics broaden our understanding of the role NO and phytoglobins play in barley during nonhost resistance against powdery mildew.
G-computation, propensity score-based methods, and targeted maximum likelihood estimator for causal inference with different covariates sets: a comparative simulation study
Authors: Chatton Arthur , Le Borgne Florent , Leyrat Clémence , Gillaizeau Florence , Rousseau Chloé , Barbin Laetitia , Laplaud David , Léger Maxime , Giraudeau Bruno , Foucher Yohann
Published: June 2020

Controlling for confounding bias is crucial in causal inference. Distinct methods are currently employed to mitigate the effects of confounding bias. Each requires the introduction of a set of covariates, which remains difficult to choose, especially regarding the different methods. We conduct a simulation study to compare the relative performance results obtained by using four different sets of covariates (those causing the outcome, those causing the treatment allocation, those causing both the outcome and the treatment allocation, and all the covariates) and four methods: g-computation, inverse probability of treatment weighting, full matching and targeted maximum likelihood estimator. Our simulations are in the context of a binary treatment, a binary outcome and baseline confounders. The simulations suggest that considering all the covariates causing the outcome led to the lowest bias and variance, particularly for g-computation. The consideration of all the covariates did not decrease the bias but significantly reduced the power. We apply these methods to two real-world examples that have clinical relevance, thereby illustrating the real-world importance of using these methods. We propose an R package RISCA to encourage the use of g-computation in causal inference.
Establishment of a guided, in vivo, multi-channel, abdominal, tissue imaging approach
Authors: Bahlmann Julia , Madrahimov Nodir , Daniel Fiene , Theidel David , DeTemple Daphne E. , Buettner Manuela , Bleich André , Haverich Axel , Heisterkamp Alexander , Kalies Stefan
Published: June 2020

Novel tools in humane animal research should benefit the animal as well as the experimentally obtained data. Imaging technologies have proven to be versatile and also in accordance with the demands of the 3 R principle. However, most imaging technologies are either limited by the target organs, number of repetitive imaging sessions, or the maximal resolution. We present a technique-, which enables multicolor abdominal imaging on a tissue level. It is based on a small imaging fiber endoscope, which is guided by a second commercial endoscope. The imaging fiber endoscope allows the distinction of four different fluorescence channels. It has a size of less than 1 mm and can approximately resolve single cells. The imaging fiber was successfully tested on cells in vitro, excised organ tissue, and in mice in vivo. Combined with neural networks for image restauration, high quality images from various abdominal organs of interest were realized. The second endoscope ensured a precise placement of the imaging fiber in vivo. Our approach of guided tissue imaging in vivo, combined with neuronal networks for image restauration, permits the acquisition of fluorescence-microscope like images with minimal invasive surgery in vivo. Therefore, it is possible to extend our approach to repetitive imaging sessions. The cost below 30 thousand euros allows an establishment of this approach in various scenarios.
Spin-splitting effects on the interband optical conductivity and activity of phosphorene
Authors: Phuong Le Thi Thu , Phong Tran C. , Yarmohammadi Mohsen
Published: June 2020

Being able to tune the anisotropic interband transitions in phosphorene at finite temperature offers an enormous amount of possibilities in finding new insights in the optoelectronic community. To contribute to this goal we propose a Zeeman spin-splitting field aiming at absorbing various frequencies of the incident light. Employing the tight-binding Hamiltonian to describe the carrier dynamics and the Kubo formalism to formulate the orientation-dependent interband optical conductivity (IOC) and optical activity of phosphorene we investigate the absorption and scattering mechanisms in phosphorene depending on the Zeeman field strength and optical energy parameters. The optical activity features are characterized by exploring the eccentricity and shift phase of reflected and transmitted electromagnetic waves of the incident light. Different electronic phases in the absence and presence of Zeeman field ultimate different types of interband transitions of which in all cases the IOC along the armchair direction is larger than the zigzag one. However, we observed an irregular (regular) process for IOC with the Zeeman field along the armchair (zigzag) direction, resulting in irregular (regular) absorption and scattering mechanisms. Additionally, a little to no effects for temperature-dependent IOC are provided with the Zeeman field in undoped phosphorene. Further, almost linearly and elliptically polarizations are reported for the transmitted and reflected waves, respectively, indicating that the phosphorene is almost transparent. The emergence of Zeeman spin-splitting effects in optoelectronic properties of phosphorene is pleasant to make it a great potential candidate for logic applications.
Noninvasive diffusion magnetic resonance imaging of brain tumour cell size for the early detection of therapeutic response
Authors: Roberts Thomas A. , Hyare Harpreet , Agliardi Giulia , Hipwell Ben , d’Esposito Angela , Ianus Andrada , Breen-Norris James O. , Ramasawmy Rajiv , Taylor Valerie , Atkinson David , Punwani Shonit , Lythgoe Mark F. , Siow Bernard , Brandner Sebastian , Rees Jeremy , Panagiotaki Eleftheria , Alexander Daniel C. , Walker-Samuel Simon
Published: June 2020

Cancer cells differ in size from those of their host tissue and are known to change in size during the processes of cell death. A noninvasive method for monitoring cell size would be highly advantageous as a potential biomarker of malignancy and early therapeutic response. This need is particularly acute in brain tumours where biopsy is a highly invasive procedure. Here, diffusion MRI data were acquired in a GL261 glioma mouse model before and during treatment with Temozolomide. The biophysical model VERDICT (Vascular Extracellular and Restricted Diffusion for Cytometry in Tumours) was applied to the MRI data to quantify multi-compartmental parameters connected to the underlying tissue microstructure, which could potentially be useful clinical biomarkers. These parameters were compared to ADC and kurtosis diffusion models, and, measures from histology and optical projection tomography. MRI data was also acquired in patients to assess the feasibility of applying VERDICT in a range of different glioma subtypes. In the GL261 gliomas, cellular changes were detected according to the VERDICT model in advance of gross tumour volume changes as well as ADC and kurtosis models. VERDICT parameters in glioblastoma patients were most consistent with the GL261 mouse model, whilst displaying additional regions of localised tissue heterogeneity. The present VERDICT model was less appropriate for modelling more diffuse astrocytomas and oligodendrogliomas, but could be tuned to improve the representation of these tumour types. Biophysical modelling of the diffusion MRI signal permits monitoring of brain tumours without invasive intervention. VERDICT responds to microstructural changes induced by chemotherapy, is feasible within clinical scan times and could provide useful biomarkers of treatment response.
Coalition-structured governance improves cooperation to provide public goods
Authors: Vasconcelos Vítor V. , Hannam Phillip M. , Levin Simon A. , Pacheco Jorge M.
Published: June 2020

While the benefits of common and public goods are shared, they tend to be scarce when contributions are provided voluntarily. Failure to cooperate in the provision or preservation of these goods is fundamental to sustainability challenges, ranging from local fisheries to global climate change. In the real world, such cooperative dilemmas occur in multiple interactions with complex strategic interests and frequently without full information. We argue that voluntary cooperation enabled across overlapping coalitions (akin to polycentricity) not only facilitates a higher generation of non-excludable public goods, but it may also allow evolution toward a more cooperative, stable, and inclusive approach to governance. Contrary to any previous study, we show that these merits of multi-coalition governance are far more general than the singular examples occurring in the literature, and they are robust under diverse conditions of excludability, congestion of the non-excludable public good, and arbitrary shapes of the return-to-contribution function. We first confirm the intuition that a single coalition without enforcement and with players pursuing their self-interest without knowledge of returns to contribution is prone to cooperative failure. Next, we demonstrate that the same pessimistic model but with a multi-coalition structure of governance experiences relatively higher cooperation by enabling recognition of marginal gains of cooperation in the game at stake. In the absence of enforcement, public-goods regimes that evolve through a proliferation of voluntary cooperative forums can maintain and increase cooperation more successfully than singular, inclusive regimes.
Abnormal Papillary Muscle Signal on Cine MRI As a Typical Feature of Mitral Valve Prolapse
Authors: Scatteia Alessandra , Pascale Carmine Emanuele , Gallo Paolo , Pezzullo Salvatore , America Raffaella , Cappelletti Alberto Maria , Dalla Vecchia Laura Adelaide , Guarini Pasquale , Dellegrottaglie Santo
Published: June 2020

Background: Mitral valve prolapse (MVP) is characterized by an abnormal movement of the valvular apparatus which may affect the papillary muscles (PMs) function and structure. Aim of the study was to investigate abnormal PM signal in MVP by using cardiac magnetic resonance imaging (MRI). Methods and Results: We enrolled 47 consecutive patients with MVP evaluated by cardiac MRI. Additional groups included healthy volunteers, patients with moderate-to-severe mitral regurgitation (not caused by MVP) and patients with hypertrophic cardiomyopathy. Visual assessment of the PM signals was carried out and the signal intensity (SI) of both the antero-lateral and postero-medial PMs was normalized by that of the left ventricular (LV) parietal myocardium. Our results show that in the MVP group only, the PM signal intensity was significantly lower compared to the one of the LV parietal myocardium. This sign did not correlate with either LV late gadolinium enhancement or positive anamnesis for significant arrhythmias. Conclusions: In MVP patients only, PM signal is significantly reduced compared to LV parietal myocardium (“darker appearance”). The described findings are not clearly related to evidence of myocardial fibrosis, as assessed by MRI, and to previous occurrence of complex ventricular arrhythmias.
Toward Simple, Predictive Understanding of Protein-Ligand Interactions: Electronic Structure Calculations on Torpedo Californica Acetylcholinesterase Join Forces with the Chemist’s Intuition
Authors: Sylvetsky Nitai
Published: June 2020

Contemporary efforts for empirically-unbiased modeling of protein-ligand interactions entail a painful tradeoff – as reliable information on both noncovalent binding factors and the dynamic behavior of a protein-ligand complex is often beyond practical limits. We demonstrate that information drawn exclusively from static molecular structures can be used for reproducing and predicting experimentally-measured binding affinities for protein-ligand complexes. In particular, inhibition constants (Ki) were calculated for seven different competitive inhibitors of Torpedo californica acetylcholinesterase using a multiple-linear-regression-based model. The latter, incorporating five independent variables – drawn from QM cluster, DLPNO-CCSD(T) calculations and LED analyses on the seven complexes, each containing active amino-acid residues found within interacting distance (3.5 Å) from the corresponding ligand – is shown to recover 99.9% of the sum of squares for measured Ki values, while having no statistically-significant residual errors. Despite being fitted to a small number of data points, leave-one-out cross-validation statistics suggest that it possesses surprising predictive value (Q2LOO=0.78, or 0.91 upon removal of a single outlier). This thus challenges ligand-invariant definitions of active sites, such as implied in the lock-key binding theory, as well as in alternatives highlighting shape-complementarity without taking electronic effects into account. Broader implications of the current work are discussed in dedicated appendices.
A single dose of eHSP72 attenuates sepsis severity in mice
Authors: Sulzbacher Maicon Machado , Sulzbacher Lucas Machado , Passos Felipe Rafael , Bilibio Bruna Letícia Endl , Althaus Wellington Felipe , Weizenmann Luana , de Oliveira Kauana , Frizzo Matias Nunes , Ludwig Mirna Stela , Heck Thiago Gomes
Published: June 2020

High levels of extracellular 72 kDa heat shock protein (eHSP72) can be detected in the serum of septic patients and are associated with increased oxidative profiles and elevated rates of mortality among these patients. However, a possible immunomodulatory role for this protein, resulting in tissue protection during sepsis, has never been assessed. In this study, we investigated whether eHSP72 administration could attenuate the severity of sepsis in a mouse peritonitis model. Animals (90-day-old male C57BL/6J mice) were divided into Sepsis (n = 8) and Sepsis + eHSP72 (n = 9) groups, which both received injections of 20% fecal solution [1 mg/g body weight (wt), intraperitoneal (i.p.)], to trigger peritonitis induced-sepsis, whereas a Control group (n = 7) received a saline injection. eHSP72 was administered (1.33 ng/g body wt) to the Sepsis+eHSP72 group, 12 h after sepsis induction. All animals were evaluated for murine sepsis score (MSS), hemogram, core temperature, and glycemia (before and 4, 12, and 24 h after sepsis induction). Treatment with eHSP72 promoted reduced sepsis severity 24 h after sepsis induction, based on MSS scores (Control = 1.14 ± 1.02; Sepsis = 11.07 ± 7.24, and Sepsis + eHSP72 = 5.62 ± 1.72, P < 0.001) and core temperatures (°C; Control = 37.48 ± 0.58; Sepsis = 35.17 ± 2.88, and Sepsis + eHSP72 = 36.94 ± 2.02; P = 0.006). eHSP72 treatment also limited the oxidative profile and respiratory dysfunction in mice with sepsis. Although sepsis modified glycemic levels and white and red blood cell counts, these variables were not influenced by eHSP72 treatment (P > 0.05). Finally, eHSP72 improved the survival rate after sepsis (P = 0.0371). Together, our results indicated that eHSP72 may ameliorate sepsis severity and possibly improve some sepsis indices in mice.
Apparent diffusion coefficient estimates based on 24 hours tracer movement support glymphatic transport in human cerebral cortex
Authors: Valnes Lars Magnus , Mitusch Sebastian K. , Ringstad Geir , Eide Per Kristian , Funke Simon W. , Mardal Kent-Andre
Published: June 2020

The recently proposed glymphatic system suggests that bulk flow is important for clearing waste from the brain, and as such may underlie the development of e.g. Alzheimer’s disease. The glymphatic hypothesis is still controversial and several biomechanical modeling studies at the micro-level have questioned the system and its assumptions. In contrast, at the macro-level, there are many experimental findings in support of bulk flow. Here, we will investigate to what extent the CSF tracer distributions seen in novel magnetic resonance imaging (MRI) investigations over hours and days are suggestive of bulk flow as an additional component to diffusion. In order to include the complex geometry of the brain, the heterogeneous CSF flow around the brain, and the transport over the time-scale of days, we employed the methods of partial differential constrained optimization to identify the apparent diffusion coefficient (ADC) that would correspond best to the MRI findings. We found that the computed ADC in the cortical grey matter was 5–26% larger than the ADC estimated with DTI, which suggests that diffusion may not be the only mechanism governing transport.
Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value
Authors: Acquadro Alberto , Barchi Lorenzo , Portis Ezio , Nourdine Mohamed , Carli Cristiano , Monge Simone , Valentino Danila , Lanteri Sergio
Published: June 2020

Sweet pepper (Capsicum annuum L.) is a high value crop and one of the most widely grown vegetables belonging to the Solanaceae family. In addition to commercial varieties and F1 hybrids, a multitude of landraces are grown, whose genetic combination is the result of hundreds of years of random, environmental, and farmer selection. High genetic diversity exists in the landrace gene pool which however has scarcely been studied, thus bounding their cultivation. We re-sequenced four pepper inbred lines, within as many Italian landraces, which representative of as many fruit types: big sized blocky with sunken apex (‘Quadrato’) and protruding apex or heart shaped (‘Cuneo’), elongated (‘Corno’) and smaller sized sub-spherical (‘Tumaticot’). Each genomic sequence was obtained through Illumina platform at coverage ranging from 39 to 44×, and reconstructed at a chromosome scale. About 35.5k genes were predicted in each inbred line, of which 22,017 were shared among them and the reference genome (accession ‘CM334’). Distinctive variations in miRNAs, resistance gene analogues (RGAs) and susceptibility genes (S-genes) were detected. A detailed survey of the SNP/Indels occurring in genes affecting fruit size, shape and quality identified the highest frequencies of variation in regulatory regions. Many structural variations were identified as presence/absence variations (PAVs), notably in resistance gene analogues (RGAs) and in the capsanthin/capsorubin synthase (CCS) gene. The large allelic diversity observed in the four inbred lines suggests their potential use as a pre-breeding resource and represents a one-stop resource for C. annuum genomics and a key tool for dissecting the path from sequence variation to phenotype.
Demographic and reproductive associations with nematode infection in a long-lived mammal
Authors: Lynsdale Carly L. , Mon Nay Oo , Franco dos Santos Diogo J. , Aung Htoo Htoo , Nyein U Kyaw , Htut Win , Childs Dylan , Lummaa Virpi
Published: June 2020

Infection by macroparasites, such as nematodes, varies within vertebrate host systems; elevated infection is commonly observed in juveniles and males, and, for females, with different reproductive states. However, while such patterns are widely recognized in short-lived model systems, how they apply to long-lived hosts is comparatively understudied. Here, we investigated how infection varies with host age, sex, and female reproduction in a semi-captive population of individually marked Asian elephantsElephas maximus. We carried out 1,977 faecal egg counts (FECs) across five years to estimate nematode loads for 324 hosts. Infection patterns followed an established age-infection curve, whereby calves (5 years) exhibited the highest FECs and adults (45 years) the lowest. However, males and females had similar FECs across their long lifespan, despite distinct differences in life-history strategy and clear sexual dimorphism. Additionally, although mothers invest two years in pregnancy and a further three to five years into lactation, nematode load did not vary with four different measures of female reproduction. Our results provide a much-needed insight into the host-parasite dynamics of a long-lived host; determining host-specific associations with infection in such systems is important for broadening our knowledge of parasite ecology and provides practical applications for wildlife medicine and management.
Aptamer based high throughput colorimetric biosensor for detection of staphylococcus aureus
Authors: Yu Tianxiao , Xu Hong , Zhao Yan , Han Yanjie , Zhang Yao , Zhang Jingrui , Xu Caihong , Wang Wenju , Guo Qing , Ge Jun
Published: June 2020

To develop a high throughput colorimetric biosensor for detection ofStaphylococcus aureus(SA) based on specific aptamer and catalysis of dsDNA-SYBR Green I (SG I) complex. SA specific aptamer was immobilized on a 96-well plate by hybridization with the capture probe anchored on the plate surface through streptavidin-biotin binding. In presence of SA, the aptamer was dissociated from the capture probe-aptamer duplex due to the stronger interaction between the aptamer and SA. The consequent single-strand capture probe could be hybridized with a three-way junction (TWJ) probe. With the presence of SG I, the dsDNA-SG I complex catalyze the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB) under photo-irradiation, producing sensitive photo-catalyzed colorimetric response to SA. Under the optimal conditions, the proposed method could directly detect SA with the limit of detection (LOD) at 81 CFU mL−1in PBS buffer in 5.5 hours, which demonstrated the sensitive and fast quantification of target pathogenic bacteria. The method showed weak colorimetric signal toEscherichia coliandPseudomonas aeruginosa, indicating the high specificity for SA. In addition, the method can simultaneously detect 96 samples which can be used for high throughput analysis. The designed method may become a powerful tool for pathogenic microorganisms screening in clinical diagnostics, food safety and environmental monitoring.
A Unique Mouse Model of Early Life Exercise Enables Hippocampal Memory and Synaptic Plasticity
Authors: Ivy Autumn S. , Yu Tim , Kramár Enikö , Parievsky Sonia , Sohn Fred , Vu Thao
Published: June 2020

Physical exercise is a powerful modulator of learning and memory. Mechanisms underlying the cognitive benefits of exercise are well documented in adult rodents. Exercise studies targeting postnatal periods of hippocampal maturation (specifically targeting periods of synaptic reorganization and plasticity) are lacking. We characterize a model of early-life exercise (ELE) in male and female mice designed with the goal of identifying critical periods by which exercise may have a lasting impact on hippocampal memory and synaptic plasticity. Mice freely accessed a running wheel during three postnatal periods: the 4th postnatal week (juvenile ELE, P21–27), 6th postnatal week (adolescent ELE, P35–41), or 4th-6th postnatal weeks (juvenile-adolescent ELE, P21–41). All exercise groups increased their running distances during ELE. When exposed to a subthreshold learning stimulus, juv ELE and juv-adol ELE formed lasting long-term memory for an object location memory task, whereas sedentary and adol ELE mice did not. Electrophysiological experiments revealed enhanced long-term potentiation in hippocampal CA1 in the juvenile-adolescent ELE group. I/O curves were also significantly modulated in all mice that underwent ELE. Our results suggest that early-life exercise, specifically during the 4th postnatal week, can enable hippocampal memory, synaptic plasticity, and alter hippocampal excitability when occurring during postnatal periods of hippocampal maturation.