bluuebunny/crossref_metadata_2025 huggingface dataset:
An Anticipation Experiment for Plate Tectonics
Authors: Gillooly Tom , Coltice Nicolas , Wolf Christian
Published: October 2019

Although plate tectonics has pushed the frontiers of geosciences in the past 50 years, it has legitimate limitations, and among them we focus on both the absence of dynamics in the theory and the difficulty of reconstructing tectonics when data are sparse. In this manuscript, we propose an anticipation experiment, proposing a singular outlook on plate tectonics in the digital era. We hypothesize that mantle convection models producing self‐consistently plate‐like behavior will capture the essence of the self‐organization of plate boundaries. Such models exist today in a preliminary fashion, and we use them here to build a database of mid‐ocean ridge and trench configurations. To extract knowledge from it, we develop a machine learning framework based on Generative Adversarial Networks (GANs) that learns the regularities of the self‐organization in order to fill gaps of observations when working on reconstructing a plate configuration. The user provides the distribution of known ridges and trenches, the location of the region where observations lack, and our digital architecture proposes a horizontal divergence map from which missing plate boundaries are extracted. Our framework is able to prolongate and interpolate plate boundaries within an unresolved region but fails to retrieve a plate boundary that would be completely contained inside of it. The attempt we make is certainly too early because geodynamic models need improvement and a larger amount of geodynamic model outputs, as independent as possible, is required. However, this work suggests applying such an approach to expand the capabilities of plate tectonics is within reach.
Epigenetic regulation of macrophages: from homeostasis maintenance to host defense
Authors: Chen Siyuan , Yang Jing , Wei Yuquan , Wei Xiawei
Published: October 2019

Macrophages are crucial members of the innate immune response and important regulators. The differentiation and activation of macrophages require the timely regulation of gene expression, which depends on the interaction of a variety of factors, including transcription factors and epigenetic modifications. Epigenetic changes also give macrophages the ability to switch rapidly between cellular programs, indicating the ability of epigenetic mechanisms to affect phenotype plasticity. In this review, we focus on key epigenetic events associated with macrophage fate, highlighting events related to the maintenance of tissue homeostasis, responses to different stimuli and the formation of innate immune memory. Further understanding of the epigenetic regulation of macrophages will be helpful for maintaining tissue integrity, preventing chronic inflammatory diseases and developing therapies to enhance host defense.
Atomic layer deposited Pt-Ru dual-metal dimers and identifying their active sites for hydrogen evolution reaction
Authors: Zhang Lei , Si Rutong , Liu Hanshuo , Chen Ning , Wang Qi , Adair Keegan , Wang Zhiqiang , Chen Jiatang , Song Zhongxin , Li Junjie , Banis Mohammad Norouzi , Li Ruying , Sham Tsun-Kong , Gu Meng , Liu Li-Min , Botton Gianluigi A. , Sun Xueliang
Published: October 2019

Single atom catalysts exhibit particularly high catalytic activities in contrast to regular nanomaterial-based catalysts. Until recently, research has been mostly focused on single atom catalysts, and it remains a great challenge to synthesize bimetallic dimer structures. Herein, we successfully prepare high-quality one-to-one A-B bimetallic dimer structures (Pt-Ru dimers) through an atomic layer deposition (ALD) process. The Pt-Ru dimers show much higher hydrogen evolution activity (more than 50 times) and excellent stability compared to commercial Pt/C catalysts. X-ray absorption spectroscopy indicates that the Pt-Ru dimers structure model contains one Pt-Ru bonding configuration. First principle calculations reveal that the Pt-Ru dimer generates a synergy effect by modulating the electronic structure, which results in the enhanced hydrogen evolution activity. This work paves the way for the rational design of bimetallic dimers with good activity and stability, which have a great potential to be applied in various catalytic reactions.
Identification of advanced spin-driven thermoelectric materials via interpretable machine learning
Authors: Iwasaki Yuma , Sawada Ryohto , Stanev Valentin , Ishida Masahiko , Kirihara Akihiro , Omori Yasutomo , Someya Hiroko , Takeuchi Ichiro , Saitoh Eiji , Yorozu Shinichi
Published: October 2019

Machine learning is becoming a valuable tool for scientific discovery. Particularly attractive is the application of machine learning methods to the field of materials development, which enables innovations by discovering new and better functional materials. To apply machine learning to actual materials development, close collaboration between scientists and machine learning tools is necessary. However, such collaboration has been so far impeded by the black box nature of many machine learning algorithms. It is often difficult for scientists to interpret the data-driven models from the viewpoint of material science and physics. Here, we demonstrate the development of spin-driven thermoelectric materials with anomalous Nernst effect by using an interpretable machine learning method called factorized asymptotic Bayesian inference hierarchical mixture of experts (FAB/HMEs). Based on prior knowledge of material science and physics, we were able to extract from the interpretable machine learning some surprising correlations and new knowledge about spin-driven thermoelectric materials. Guided by this, we carried out an actual material synthesis that led to the identification of a novel spin-driven thermoelectric material. This material shows the largest thermopower to date.
Publisher Correction: Social Closure and the Evolution of Cooperation via Indirect Reciprocity
Authors: Righi Simone , Takács Károly
Published: October 2019

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
The first amber caridean shrimp from Mexico reveals the ancient adaptation of the Palaemon to the mangrove estuary environment
Authors: Du Bao-Jie , Chen Rui , Li Xin-Zheng , Tao Wen-Tao , Bu Wen-Jun , Xiao Jin-Hua , Huang Da-Wei
Published: October 2019

The aquatic and semiaquatic invertebrates in fossiliferous amber have been reported, including taxa in a wide range of the subphylum Crustacea of Arthropoda. However, no caridean shrimp has been discovered so far in the world. The shrimp Palaemon aestuarius sp. nov. (Palaemonidae) preserved in amber from Chiapas, Mexico during Early Miocene (ca. 22.8 Ma) represents the first and the oldest amber caridean species. This finding suggests that the genus Palaemon has occupied Mexico at least since Early Miocene. In addition, the coexistence of the shrimp, a beetle larva, and a piece of residual leaf in the same amber supports the previous explanations for the Mexican amber depositional environment, in the tide-influenced mangrove estuary region.
Recreational vessels without Automatic Identification System (AIS) dominate anthropogenic noise contributions to a shallow water soundscape
Authors: Hermannsen Line , Mikkelsen Lonnie , Tougaard Jakob , Beedholm Kristian , Johnson Mark , Madsen Peter T.
Published: October 2019

Recreational boating is an increasing activity in coastal areas and its spatiotemporal overlap with key habitats of marine species pose a risk for negative noise impacts. Yet, recreational vessels are currently unaccounted for in vessel noise models using Automatic Identification System (AIS) data. Here we conduct a case study investigating noise contributions from vessels with and without AIS (non-AIS) in a shallow coastal area within the Inner Danish waters. By tracking vessels with theodolite and AIS, while recording ambient noise levels, we find that non-AIS vessels have a higher occurrence (83%) than AIS vessels, and that motorised recreational vessels can elevate third-octave band noise centred at 0.125, 2 and 16 kHz by 47–51 dB. Accordingly, these vessels dominated the soundscape in the study site due to their high numbers, high speeds and proximity to the coast. Furthermore, recreational vessels caused 49–85% of noise events potentially eliciting behavioural responses in harbour porpoises (AIS vessels caused 5–24%). We therefore conclude that AIS data would poorly predict vessel noise pollution and its impacts in this and other similar marine environments. We suggest to improve vessel noise models and impact assessments by requiring that faster and more powerful recreational vessels carry AIS-transmitters.
Volume explored by a branching random walk on general graphs
Authors: Bordeu Ignacio , Amarteifio Saoirse , Garcia-Millan Rosalba , Walter Benjamin , Wei Nanxin , Pruessner Gunnar
Published: October 2019

Branching processes are used to model diverse social and physical scenarios, from extinction of family names to nuclear fission. However, for a better description of natural phenomena, such as viral epidemics in cellular tissues, animal populations and social networks, a spatial embedding—the branching random walk (BRW)—is required. Despite its wide range of applications, the properties of the volume explored by the BRW so far remained elusive, with exact results limited to one dimension. Here we present analytical results, supported by numerical simulations, on the scaling of the volume explored by a BRW in the critical regime, the onset of epidemics, in general environments. Our results characterise the spreading dynamics on regular lattices and general graphs, such as fractals, random trees and scale-free networks, revealing the direct relation between the graphs’ dimensionality and the rate of propagation of the viral process. Furthermore, we use the BRW to determine the spectral properties of real social and metabolic networks, where we observe that a lack of information of the network structure can lead to differences in the observed behaviour of the spreading process. Our results provide observables of broad interest for the characterisation of real world lattices, tissues, and networks.
Acceleration of mass transfer processes in plants due to the geometric structure: a fractional order equation of mass transfer and its application
Authors: Arkhincheev V. E.
Published: October 2019

The problem of mass transfer in living plants in the framework of the comb model was studied. The fractional order equation for problem of mass transfer was deduced and its application for transfer in the plants was considered. The different temporal asymptotic, which occurred due to geometry of plants, were obtained. It was established that mass transfer processes in living plants depend on the geometric structure of plants, namely, it is mass transfer is accelerated from steam to branches. The discussion of obtained results was given.
Incorporation of fragmented visuo-olfactory episodic memory into dreams and its association with memory performance
Authors: Plailly J. , Villalba M. , Vallat R. , Nicolas A. , Ruby P.
Published: October 2019

The question of a possible link between dream content and memory consolidation remains open. After a comprehensive review of the literature, we present novel findings from an experiment testing whether the incorporation of recently learned stimuli into dream reports is associated with improved post-sleep memory performance. Thirty-two high dream recallers freely explored new visuo-olfactory episodes for 3 consecutive days. During the nights following each non-explicit encoding, participants wore a wrist actimeter, and woke up at 5am and their usual waking time to record their dreams (intensity of all oneiric sensory perception was assessed using scales). A total of 120 dreams were reported and elements related to the encoding phase were identified in 37 of them, either learning-related (mainly visual- and rarely olfactory-related elements), or experiment-related (lab- or experimenters-related elements). On the 4th day, we found that participants with learning-related (n = 16) and participants with learning-related and/or experiment-related dreams (n = 21) had similar odor recognition and odor-evoked episodic memory with the other participants. However, they had significantly better visuo-spatial memory of the episodes in comparison to the other participants. Our results support the hypothesis that the learning phase is loosely incorporated into dreams and that this incorporation is associated with sleep related memory consolidation.
Detection and identification of transgenic events by next generation sequencing combined with enrichment technologies
Authors: Debode Frédéric , Hulin Julie , Charloteaux Benoît , Coppieters Wouter , Hanikenne Marc , Karim Latifa , Berben Gilbert
Published: October 2019

Next generation sequencing (NGS) is a promising tool for analysing the quality and safety of food and feed products. The detection and identification of genetically modified organisms (GMOs) is complex, as the diversity of transgenic events and types of structural elements introduced in plants continue to increase. In this paper, we show how a strategy that combines enrichment technologies with NGS can be used to detect a large panel of structural elements and partially or completely reconstruct the new sequence inserted into the plant genome in a single analysis, even at low GMO percentages. The strategy of enriching sequences of interest makes the approach applicable even to mixed products, which was not possible before due to insufficient coverage of the different genomes present. This approach is also the first step towards a more complete characterisation of agrifood products in a single analysis.
Detecting TP53 mutations in diagnostic and archival liquid-based Pap samples from ovarian cancer patients using an ultra-sensitive ddPCR method
Authors: Arildsen Nicolai Skovbjerg , Martin de la Fuente Laura , Måsbäck Anna , Malander Susanne , Forslund Ola , Kannisto Päivi , Hedenfalk Ingrid
Published: October 2019

High-grade serous ovarian cancer (HGSOC) is the most common subtype of epithelial ovarian cancer and early detection is challenging. TP53 mutations are a hallmark of HGSOC and detection of these mutations in liquid-based Pap samples could provide a method for early diagnosis. Here we evaluate the use of IBSAFE, an ultra-sensitive droplet digital PCR (ddPCR) method, for detecting TP53 mutations in liquid-based Pap samples collected from fifteen women at the time of diagnosis (diagnostic samples) and/or up to seven years prior to diagnosis (archival samples). We analysed tumours for somatic TP53 mutations with next generation sequencing and were able to detect the corresponding mutations in diagnostic samples from six of eight women, while one patient harboured a germline mutation. We further detected a mutation in an archival sample obtained 20 months prior to the ovarian cancer diagnosis. The custom designed IBSAFE assays detected minor allele frequencies (MAFs) with very high assay sensitivity (MAF = 0.0068%) and were successful despite low DNA abundance (0.17–206.14 ng, median: 17.27 ng). These results provide support for further evaluation of archival liquid-based Pap samples for diagnostic purposes and demonstrate that ultra-sensitive ddPCR should be evaluated for ovarian cancer screening in high-risk groups or in the recurrent setting.
Statistical treatment of Photoluminescence Quantum Yield Measurements
Authors: Fries Felix , Reineke Sebastian
Published: October 2019

The photoluminescence quantum yield (PLQY) is an important measure of luminescent materials. Referring to the number of emitted photons per absorbed photons, it is an essential parameter that allows for primary classification of materials and further is a quantity that is of utmost importance for many detailed analyses of luminescent systems and processes. Determining the PLQY has been discussed in literature for many years and various methods are known. Absolute values can be measured directly using an appropriate setup. As this relies on the correct evaluation of photon-counts, it is a very sensitive method. Hence, systematic errors that can occur are discussed widely. However, of course those measurements also contain random uncertainties, which remain mainly unconsidered. The careful evaluation of both systematic and statistical errors of the PLQY is the only way to gain confidence in its absolute value. Here, we propose a way of evaluating the statistical uncertainty in absolute PLQY measurements. This relies on the combination of multiple measurements and the subsequent calculus of the weighted mean. The statistical uncertainty is then obtained as the standard deviation of the mean. This method not only quantifies the impact of statistical influences on the measurements, but also allows simple analysis of time-dependent systematic errors during the measurement and the identification of outliers.
Fragile X syndrome carrier screening in pregnant women in Chinese Han population
Authors: Hung Chia-Cheng , Lee Chien-Nan , Wang Yu-Chu , Chen Chih-Ling , Lin Tze-Kang , Su Yi-Ning , Lin Ming-Wei , Kang Jessica , Tai Yi-Yun , Hsu Wen-Wei , Lin Shin-Yu
Published: October 2019

Fragile X syndrome (FXS) is the most frequent genetic cause of intellectual disability (ID). It was previously believed that the FXS prevalence was low in Chinese population, and the cost-efficiency of FXS carrier screening was questioned. This retrospective observational study was conducted between September 2014 and May 2017 to determine the prevalence of FXS carriers in a large Chinese cohort of pregnant women. The FMR1 CGG repeat status was determined in 20,188 pregnant Taiwanese women and we identified 26 women with premutation (PM). The PM allele was transmitted to the fetus in 17 pregnancies (56.6%), and six of 17 expanded to full mutation (FM). One asymptomatic woman had a FM allele with 280 CGG repeats. Prenatal genetic diagnosis of her first fetus revealed a male carrying a FMR1 gene deletion of 5′ UTR and exon 1. Her second fetus was a female carrying a FM allele as well. This is so far the largest study of the FXS carrier screening in Chinese women. The prevalence of premutation allele for FXS in normal asymptomatic Taiwanese women was found to be as high as 0.13% (1 in 777) in this study. The empirical evidence suggests that reproductive FXS carrier screening in Taiwan might be cost-effective.
Rapid Brain Responses to Familiar vs. Unfamiliar Music – an EEG and Pupillometry study
Authors: Jagiello Robert , Pomper Ulrich , Yoneya Makoto , Zhao Sijia , Chait Maria
Published: October 2019

Human listeners exhibit marked sensitivity to familiar music, perhaps most readily revealed by popular “name that tune” games, in which listeners often succeed in recognizing a familiar song based on extremely brief presentation. In this work, we used electroencephalography (EEG) and pupillometry to reveal the temporal signatures of the brain processes that allow differentiation between a familiar, well liked, and unfamiliar piece of music. In contrast to previous work, which has quantified gradual changes in pupil diameter (the so-called “pupil dilation response”), here we focus on the occurrence of pupil dilation events. This approach is substantially more sensitive in the temporal domain and allowed us to tap early activity with the putative salience network. Participants (N = 10) passively listened to snippets (750 ms) of a familiar, personally relevant and, an acoustically matched, unfamiliar song, presented in random order. A group of control participants (N = 12), who were unfamiliar with all of the songs, was also tested. We reveal a rapid differentiation between snippets from familiar and unfamiliar songs: Pupil responses showed greater dilation rate to familiar music from 100–300 ms post-stimulus-onset, consistent with a faster activation of the autonomic salience network. Brain responses measured with EEG showed a later differentiation between familiar and unfamiliar music from 350 ms post onset. Remarkably, the cluster pattern identified in the EEG response is very similar to that commonly found in the classic old/new memory retrieval paradigms, suggesting that the recognition of brief, randomly presented, music snippets, draws on similar processes.
RETRACTED ARTICLE: Transplantation of Mouse Induced Pluripotent Stem Cell-Derived Podocytes in a Mouse Model of Membranous Nephropathy Attenuates Proteinuria
Authors: Ahmadi Amin , Moghadasali Reza , Ezzatizadeh Vahid , Taghizadeh Zeinab , Nassiri Seyed Mahdi , Asghari-Vostikolaee Mohammad Hassan , Alikhani Mehdi , Hadi Fatemeh , Rahbarghazi Reza , Yazdi Reza Salman , Baharvand Hossein , Aghdami Nasser
Published: October 2019

Injury to podocytes is a principle cause of initiation and progression of both immune and non-immune mediated glomerular diseases that result in proteinuria and decreased function of the kidney. Current advances in regenerative medicine shed light on the therapeutic potential of cell-based strategies for treatment of such disorders. Thus, there is hope that generation and transplantation of podocytes from induced pluripotent stem cells (iPSCs), could potentially be used as a curative treatment for glomerulonephritis caused by podocytes injury and loss. Despite several reports on the generation of iPSC-derived podocytes, there are rare reports about successful use of these cells in animal models. In this study, we first generated a model of anti-podocyte antibody-induced heavy proteinuria that resembled human membranous nephropathy and was characterized by the presence of sub-epithelial immune deposits and podocytes loss. Thereafter, we showed that transplantation of functional iPSC-derived podocytes following podocytes depletion results in recruitment of iPSC-derived podocytes within the damaged glomerulus, and leads to attenuation of proteinuria and histological alterations. These results provided evidence that application of iPSCs-derived renal cells could be a possible therapeutic strategy to favorably influence glomerular diseases outcomes.
dendPoint: a web resource for dendrimer pharmacokinetics investigation and prediction
Authors: Kaminskas Lisa M. , Pires Douglas E. V. , Ascher David B.
Published: October 2019

Nanomedicine development currently suffers from a lack of efficient tools to predict pharmacokinetic behavior without relying upon testing in large numbers of animals, impacting success rates and development costs. This work presents dendPoint, the first in silico model to predict the intravenous pharmacokinetics of dendrimers, a commonly explored drug vector, based on physicochemical properties. We have manually curated the largest relational database of dendrimer pharmacokinetic parameters and their structural/physicochemical properties. This was used to develop a machine learning-based model capable of accurately predicting pharmacokinetic parameters, including half-life, clearance, volume of distribution and dose recovered in the liver and urine. dendPoint successfully predicts dendrimer pharmacokinetic properties, achieving correlations of up to r = 0.83 and Q2 up to 0.68. dendPoint is freely available as a user-friendly web-service and database at http://biosig.unimelb.edu.au/dendpoint. This platform is ultimately expected to be used to guide dendrimer construct design and refinement prior to embarking on more time consuming and expensive in vivo testing.
Extreme sampling design in genetic association mapping of quantitative trait loci using balanced and unbalanced case-control samples
Authors: Li Yi , Levran Orna , Kim JongJoo , Zhang Tiejun , Chen Xingdong , Suo Chen
Published: October 2019

It is extremely expensive to conduct large sample size array- or sequencing based genome scale association studies. For a quantitative trait, an extreme case-control study design may improve the power and reduce the cost of variant calling. We investigated the performance of extreme study design when various proportions of samples are selected from the tails of phenotype distribution. Using simulations, we show that when risk genotypes become rare in the population and effect size is relatively small, it is beneficial to carry out an extreme sampling study. In particular, the number of selected cases and controls can even be unbalanced such that power is further increased, compared with a balanced selection. Our application to two data sets: methadone dose data and yearling weight data, demonstrated that similar results for full data analysis can be obtained using extreme sampling with only a fraction of the data. Using power analysis with simulated data and an experimental data application, we conclude that when full data is unavailable due to restricted budget, it is rewarding to employ an extreme sampling design in the sense that there can be immense cost reductions and qualitatively similar power as in the full data analysis.
A MultiTEP platform-based epitope vaccine targeting the phosphatase activating domain (PAD) of tau: therapeutic efficacy in PS19 mice
Authors: Hovakimyan Armine , Antonyan Tatevik , Shabestari Sepideh Kiani , Svystun Olga , Chailyan Gor , Coburn Morgan A. , Carlen-Jones William , Petrushina Irina , Chadarevian Jean Paul , Zagorski Karen , Petrovsky Nikolai , Cribbs David H. , Agadjanyan Michael G. , Ghochikyan Anahit , Davtyan Hayk
Published: October 2019

Pathological tau correlates well with cognitive impairments in Alzheimer’s disease (AD) patients and therefore represents a promising target for immunotherapy. Targeting an appropriate B cell epitope in pathological tau could in theory produce an effective reduction of pathology without disrupting the function of normal native tau. Recent data demonstrate that the N-terminal region of tau (aa 2-18), termed the “phosphatase activation domain (PAD)”, is hidden within native Tau in a ‘paperclip’-like conformation. Conversely, PAD is exposed in pathological tau and plays an essential role in the inhibition of fast axonal transport and tau polymerization. Thus, we hypothesized that anti-tau2-18 antibodies may safely and specifically reduce pathological tau and prevent further aggregation, which in turn would neutralize tau toxicity. Therefore, we evaluated the immunogenicity and therapeutic efficacy of our MultiTEP platform-based vaccine targeting tau2-18 formulated with AdvaxCpG adjuvant (AV-1980R/A) in PS19 tau transgenic mice. The AV-1980R/A induced extremely high antibody responses and the resulting sera recognized neurofibrillary tangles and plaque-associated dystrophic neurites in AD brain sections. In addition, under non-denaturing conditions AV-1980R/A sera preferentially recognized AD-associated tau. Importantly, vaccination also prevented age-related motor and cognitive deficits in PS19 mice and significantly reduced insoluble total and phosphorylated tau species. Taken together, these findings suggest that predominantly targeting misfolded tau with AV-1980R/A could represent an effective strategy for AD immunotherapy.
Drought-induced Suppression of Female Fecundity in a Capital Breeder
Authors: Smith Charles F. , Schuett Gordon W. , Reiserer Randall S. , Dana Catherine E. , Collyer Michael L. , Davis Mark A.
Published: October 2019

Human-induced global climate change is exerting increasingly strong selective pressures on a myriad of fitness traits that affect organisms. These traits, in turn, are influenced by a variety of environmental parameters such as temperature and precipitation, particularly in ectothermic taxa such as amphibians and reptiles. Over the past several decades, severe and prolonged episodes of drought are becoming commonplace throughout North America. Documentation of responses to this environmental crisis, however, is often incomplete, particularly in cryptic species. Here, we investigated reproduction in a population of pitviper snakes (copperhead,Agkistrodon contortrix), a live-bearing capital breeder. This population experienced a severe drought from 2012 through 2016. We tested whether declines in number of progeny were linked to this drought. Decline in total number offspring was significant, but offspring length and mass were unaffected. Reproductive output was positively impacted by precipitation and negatively impacted by high temperatures. We hypothesized that severe declines of prey species (e.g., cicada, amphibians, and small mammals) reduced energy acquisition during drought, negatively impacting reproductive output of the snakes. Support for this view was found using the periodical cicada (Magicicadaspp.) as a proxy for prey availability. Various climate simulations, including our own qualitative analysis, predict that drought events will continue unabated throughout the geographic distribution of copperheads which suggests that long-term monitoring of populations are needed to better understand geographic variation in drought resilience and cascading impacts of drought phenomena on ecosystem function.
Focal segmental glomerulosclerosis ACTN4 mutants binding to actin: regulation by phosphomimetic mutations
Authors: Shao Hanshuang , Wingert Bentley , Weins Astrid , Pollak Martin R. , Camacho Carlos , Wells Alan
Published: October 2019

Natural mutations such as lysine 255 to glutamic acid (K to E), threonine 259 to isoleucine (T to I) and serine 262 to proline (S to P) that occur within the actin binding domain of alpha-actinin-4 (ACTN4) cause an autosomal dominant form of focal segmental glomerulosclerosis (FSGS) in affected humans. This appears due to elevated actin binding propensity in podocytes resulting in a ‘frozen’ cytoskeleton. What is challenging is how this cellular behavior would be compatible with other cell functions that rely on cytoskeleton plasticity. Our previous finding revealed that wild type ACTN4 can be phosphorylated at tyrosine 4 and 31 upon stimulation by epidermal growth factor (EGF) to reduce the binding to actin cytoskeleton. We queried whether the elevated actin binding activity of FSGS mutants can be downregulated by EGF-mediated phosphorylation, to discern a mechanism by which the actin-cytoskeleton can be released in FSGS. In this manuscript, we first constructed variants with Y4/31E to mimic the phosphorylation at tyrosines 4 and 31 based on earlier modeling simulations that predicted that this would bury the actin binding domains and lead to a decrease in actin binding activity. We found that Y4/31E significantly reduced the actin binding activity of K255E, T259I and S262P, dramatically preventing them from aggregating in, and inhibiting motility of, podocytes, fibroblasts and melanoma cells. A putative kinase target site at Y265 in the actin binding domain was also generated as a phosphomimetic ACTN4 Y265E that demonstrated even greater binding to actin filaments than K255E and the other FSGS mutants. That the tyrosine kinase regulation of FSGS mutation binding to actin filaments can occur in cells was shown by phosphorylation on Y4 and Y31 of the K225E after extended exposure of cells to EGF, with a decrease in ACTN4 aggregates in fibroblasts. These findings will provide evidence for targeting the N-termini of FSGS ACTN4 mutants to downregulate their actin binding activities for ameliorating the glomerulosclerotic phenotype of patients.
Regenerable Acidity of Graphene Oxide in Promoting Multicomponent Organic Synthesis
Authors: Ebajo Virgilio D. , Santos Cybele Riesse L. , Alea Glenn V. , Lin Yuya A. , Chen Chun-Hu
Published: October 2019

The Brønsted acidity of graphene oxide (GO) materials has shown promising activity in organic synthesis. However, roles and functionality of Lewis acid sites remain elusive. Herein, we reported a carbocatalytic approach utilizing both Brønsted and Lewis acid sites in GOs as heterogeneous promoters in a series of multicomponent synthesis of triazoloquinazolinone compounds. The GOs possessing the highest degree of oxidation, also having the highest amounts of Lewis acid sites, enable optimal yields (up to 95%) under mild and non-toxic reaction conditions (85 °C in EtOH). The results of FT-IR spectroscopy, temperature-programed decomposition mass spectrometry, and X-ray photoelectron spectroscopy identified that the apparent Lewis acidity via basal plane epoxide ring opening, on top of the saturated Brønsted acidic carboxylic groups, is responsible for the enhanced carbocatalytic activities involving Knoevenagel condensation pathway. Recycled GO can be effectively regenerated to reach 97% activity of fresh GO, supporting the recognition of GO as pseudocatalyst in organic synthesis.
LXRβ controls glioblastoma cell growth, lipid balance, and immune modulation independently of ABCA1
Authors: Patel Deven , Ahmad Fahim , Kambach Diane M. , Sun Qian , Halim Alan S. , Kramp Tamalee , Camphausen Kevin A. , Stommel Jayne M.
Published: October 2019

Cholesterol is a critical component of membranes and a precursor for hormones and other signaling molecules. Previously, we showed that unlike astrocytes, glioblastoma cells do not downregulate cholesterol synthesis when plated at high density. In this report, we show that high cell density induces ABCA1 expression in glioblastoma cells, enabling them to get rid of excess cholesterol generated by an activated cholesterol biosynthesis pathway. Because oxysterols are agonists for Liver X Receptors (LXRs), we investigated whether increased cholesterol activates LXRs to maintain cholesterol homeostasis in highly-dense glioblastoma cells. We observed that dense cells had increased oxysterols, which activated LXRβ to upregulate ABCA1. Cells with CRISPR-mediated knockdown of LXRβ, but not ABCA1, had decreased cell cycle progression and cell survival, and decreased feedback repression of the mevalonate pathway in densely-plated glioma cells. LXRβ gene expression poorly correlates with ABCA1 in glioblastoma patients, and expression of each gene correlates with poor patient prognosis in different prognostic subtypes. Finally, gene expression and lipidomics analyses cells revealed that LXRβ regulates the expression of immune response gene sets and lipids known to be involved in immune modulation. Thus, therapeutic targeting of LXRβ in glioblastoma might be effective through diverse mechanisms.
Potential of recombinant Mycobacterium paragordonae expressing HIV-1 Gag as a prime vaccine for HIV-1 infection
Authors: Kim Byoung-Jun , Kim Bo-Ram , Kook Yoon-Hoh , Kim Bum-Joon
Published: October 2019

Recombinant Mycobacterium strains such as recombinant BCG (rBCG) have received considerable attention for the HIV-1 vaccine development. Recently, we described a temperature-sensitive Mycobacterium paragordonae (Mpg) strain as a novel live tuberculosis vaccine that is safer and showed an enhanced protective effect against mycobacterial infection compared to BCG. We studied the possibility of developing a vaccine against HIV-1 infection using rMpg strain expressing the p24 antigen (rMpg-p24). We observed that rMpg-p24 can induce an increased p24 expression in infected antigen presenting cells (APCs) compared to rBCG-p24. We also observed that rMpg-p24 can induce enhanced p24 specific immune responses in vaccinated mice as evidenced by increased p24-specific T lymphocyte proliferation, gamma interferon induction, antibody production and cytotoxic T lymphocyte (CTL) responses. Furthermore, an rMpg-p24 prime and plasmid DNA boost showed an increased CTL response and antibody production compared to rBCG or rMpg alone. In summary, our study indicates that a live rMpg-p24 strain induced enhanced immune responses against HIV-1 Gag in vaccinated mice. Thus, rMpg-p24 may have potential as a preventive prime vaccine in a heterologous prime-boost regimen for HIV-1 infection.
In vivo fluorescence imaging of conjunctival goblet cells
Authors: Kim Seonghan , Lee Seunghun , Chang Hoonchul , Kim Moses , Kim Myoung Joon , Kim Ki Hean
Published: October 2019

Conjunctival goblet cells (GCs) are specialized epithelial cells that secrete mucins onto the ocular surface to maintain the wet environment. Assessment of GCs is important because various ocular surface diseases are associated with their loss. Although there are GC assessment methods available, the current methods are either invasive or difficult to use. In this report, we developed a simple and non-invasive GC assessment method based on fluorescence imaging. Moxifloxacin ophthalmic solution was used to label GCs via topical administration, and then various fluorescence microscopies could image GCs in high contrasts. Fluorescence imaging of GCs in the mouse conjunctiva was confirmed by both confocal reflection microscopy and histology with Periodic acid-Schiff (PAS) labeling. Real-time in-vivo conjunctival GC imaging was demonstrated in a rat model by using both confocal fluorescence microscopy and simple wide-field fluorescence microscopy. Different GC densities were observed in the forniceal and bulbar conjunctivas of the rat eye. Moxifloxacin based fluorescence imaging provides high-contrast images of conjunctival GCs non-invasively and could be useful for the study or diagnosis of GC related ocular surface diseases.
IRAK3 modulates downstream innate immune signalling through its guanylate cyclase activity
Authors: Freihat L. A. , Wheeler J. I. , Wong A. , Turek I. , Manallack D. T. , Irving H. R.
Published: October 2019

Interleukin-1 receptor associated kinase 3 (IRAK3) is a cytoplasmic homeostatic mediator of inflammatory responses and is potentially useful as a prognostic marker in inflammation. IRAK3 inhibits signalling cascades downstream of myddosome complexes associated with toll like receptors. IRAK3 contains a death domain that interacts with other IRAK family members, a pseudokinase domain and a C-terminus domain involved with tumour necrosis factor receptor associated factor 6 (TRAF6). Previous bioinformatic studies revealed that IRAK3 contained a guanylate cyclase centre in its pseudokinase domain but its role in IRAK3 action is unresolved. We demonstrate that wildtype IRAK3 is capable of producing cGMP. Furthermore, we show that a specific point mutation in the guanylate cyclase centre reduced cGMP production. Cells containing toll like receptor 4 and a nuclear factor kappa-light-chain-enhancer of activated B cells (NFĸB) reporter system were transfected with IRAK3 or mutant IRAK3 proteins. Cell-permeable cGMP treatment of untransfected control cells suppresses downstream signalling through modulation of the NFĸB in the presence of lipopolysaccharides. Cells transfected with wildtype IRAK3 also suppress lipopolysaccharide induced NFĸB activity in the absence of exogenous cGMP. Lipopolysaccharide induced NFĸB activity was not suppressed in cells transfected with the IRAK3 mutant with reduced cGMP-generating capacity. Whereas in the presence of exogenously applied cell-permeable cGMP the IRAK3 mutant was able to retain its function by suppressing lipopolysaccharide induced NFĸB activity. Furthermore, increasing the amount of membrane permeable cGMP did not affect IRAK3’s ability to reduce NFĸB activity. These results suggest that cGMP generated by IRAK3 may be involved in regulatory function of the protein where the presence of cGMP may selectively affect downstream signalling pathway(s) by modulating binding and/or activity of nearby proteins that interact in the inflammatory signalling cascade.
How does timing of flowering affect competition for pollinators, flower visitation and seed set in an early spring grassland plant?
Authors: Kehrberger Sandra , Holzschuh Andrea
Published: October 2019

Knowledge on how the timing of flowering is related to plant fitness and species interactions is crucial to understand consequences of phenological shifts as they occur under climate change. Early flowering plants may face advantages of low competition for pollinators and disadvantages of low pollinator abundances and unfavourable weather conditions. However, it is unknown how this trade-off changes over the season and how the timing affects reproductive success. On eight grasslands we recorded intra-seasonal changes in pollinators, co-flowering plants, weather conditions, flower visitation rates, floral longevity and seed set ofPulsatilla vulgaris. Although bee abundances and the number of pollinator-suitable hours were low at the beginning of the season, early flowers ofP. vulgarisreceived higher flower visitation rates and estimated total number of bee visits than later flowers, which was positively related to seed set. Flower visitation rates decreased over time and with increasing number of co-flowering plants, which competed withP. vulgarisfor pollinators. Low interspecific competition for pollinators seems to be a major driver for early flowering dates. Thus, non-synchronous temporal shifts of co-flowering plants as they may occur under climate warming can be expected to strongly affect plant-pollinator interactions and the fitness of the involved plants.
High fusibility and chimera prevalence in an invasive colonial ascidian
Authors: Casso Maria , Tagliapietra Davide , Turon Xavier , Pascual Marta
Published: October 2019

The formation of chimeric entities through colony fusion has been hypothesized to favour colonisation success and resilience in modular organisms. In particular, it can play an important role in promoting the invasiveness of introduced species. We studied prevalence of chimerism and performed fusion experiments in Mediterranean populations of the worldwide invasive colonial ascidian Didemnum vexillum. We analysed single zooids by whole genome amplification and genotyping-by-sequencing and obtained genotypic information for more than 2,000 loci per individual. In the prevalence study, we analysed nine colonies and identified that 44% of them were chimeric, composed of 2–3 different genotypes. In the fusion experiment 15 intra- and 30 intercolony pairs were assayed but one or both fragments regressed and died in ~45% of the pairs. Among those that survived for the length of the experiment (30 d), 100% isogeneic and 31% allogeneic pairs fused. Fusion was unlinked to global genetic relatedness since the genetic distance between fused or non-fused intercolony pairs did not differ significantly. We could not detect any locus directly involved in allorecognition, but we cannot preclude the existence of a histocompatibility mechanism. We conclude that chimerism occurs frequently in D. vexillum and may be an important factor to enhance genetic diversity and promote its successful expansion.
Polymer-Salt Aqueous Two-Phase System (ATPS) Micro-Droplets for Cell Encapsulation
Authors: Mastiani Mohammad , Firoozi Negar , Petrozzi Nicholas , Seo Seokju , Kim Myeongsub
Published: October 2019

Biosample encapsulation is a critical step in a wide range of biomedical and bioengineering applications. Aqueous two-phase system (ATPS) droplets have been recently introduced and showed a great promise to the biological separation and encapsulation due to their excellent biocompatibility. This study shows for the first time the passive generation of salt-based ATPS microdroplets and their biocompatibility test. We used two ATPS including polymer/polymer (polyethylene glycol (PEG)/dextran (DEX)) and polymer/salt (PEG/Magnesium sulfate) for droplet generation in a flow-focusing geometry. Droplet morphologies and monodispersity in both systems are studied. The PEG/salt system showed an excellent capability of uniform droplet formation with a wide range of sizes (20–60 μm) which makes it a suitable candidate for encapsulation of biological samples. Therefore, we examined the potential application of the PEG/salt system for encapsulating human umbilical vein endothelial cells (HUVECs). A cell viability test was conducted on MgSO4 solutions at various concentrations and our results showed an adequate cell survival. The findings of this research suggest that the polymer/salt ATPS could be a biocompatible all-aqueous platform for cell encapsulation.
Responses to Quadrivalent Influenza Vaccine Reveal Distinct Circulating CD4+CXCR5+ T Cell Subsets in Men Living with HIV
Authors: Cole Megan E. , Saeed Zainab , Shaw A. Torm , Guo Yanping , Höschler Katja , Winston Alan , Cooke Graham S. , Fidler Sarah , Taylor Graham P. , Pollock Katrina M.
Published: October 2019

T cell help for B cells may be perturbed in people living with HIV (PLWH), even when HIV is suppressed, as evidenced by reports of suboptimal responses to influenza vaccination. We investigated cTFH responses to the 2017–18 inactivated quadrivalent influenza vaccine (QIV) in men living with antiretroviral therapy (ART)-suppressed HIV infection who were treated in the early or chronic phase of infection, and control subjects. Here we show that seroprotective antibody responses in serum and oral fluid correlated with cTFH activation and were equivalent in all three groups, irrespective of when ART was started. These responses were attenuated in those reporting immunisation with influenza vaccine in the preceding three years, independent of HIV infection. Measurement of influenza-specific IgG in oral fluid was closely correlated with haemagglutination inhibition titre. T-SNE and two-dimensional analysis revealed a subset of CD4+CXCR3+CXCR5+ cTFH activated at one week after vaccination. This was distinguishable from cTFH not activated by vaccination, and a rare, effector memory CD4+CXCR5hiCD32hi T cell subset. The data support the use of QIV for immunisation of PLWH, reveal distinct circulating CD4+CXCR5+ T cell subsets and demonstrate oral fluid sampling for influenza-specific IgG is an alternative to phlebotomy.
Diamond Etching Beyond 10 μm with Near-Zero Micromasking
Authors: Hicks Marie-Laure , Pakpour-Tabrizi Alexander C. , Jackman Richard B.
Published: October 2019

To exploit the exceptional properties of diamond, new high quality fabrication techniques are needed to produce high performing devices. Etching and patterning diamond to depths beyond one micron has proven challenging due to the hardness and chemical resistance of diamond. A new cyclic Ar/O2 - Ar/Cl2 ICP RIE process has been developed to address micromasking issues from the aluminium mask by optimising the proportion of O2 in the plasma and introducing a preferential “cleaning” step. High quality smooth features up to, but not limited to, 10.6 μm were produced with an average etched surface roughness of 0.47 nm at a diamond etch rate of 45 nm/min and 16.9:1 selectivity.
Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies
Authors: Alexaki Aikaterini , Hettiarachchi Gaya K. , Athey John C. , Katneni Upendra K. , Simhadri Vijaya , Hamasaki-Katagiri Nobuko , Nanavaty Puja , Lin Brian , Takeda Kazuyo , Freedberg Darón , Monroe Dougald , McGill Joseph R. , Peters Robert , Kames Jacob M. , Holcomb David D. , Hunt Ryan C. , Sauna Zuben E. , Gelinas Amy , Janjic Nebojsa , DiCuccio Michael , Bar Haim , Komar Anton A. , Kimchi-Sarfaty Chava
Published: October 2019

Synonymous codons occur with different frequencies in different organisms, a phenomenon termed codon usage bias. Codon optimization, a common term for a variety of approaches used widely by the biopharmaceutical industry, involves synonymous substitutions to increase protein expression. It had long been presumed that synonymous variants, which, by definition, do not alter the primary amino acid sequence, have no effect on protein structure and function. However, a critical mass of reports suggests that synonymous codon variations may impact protein conformation. To investigate the impact of synonymous codons usage on protein expression and function, we designed an optimized coagulation factor IX (FIX) variant and used multiple methods to compare its properties to the wild-type FIX upon expression in HEK293T cells. We found that the two variants differ in their conformation, even when controlling for the difference in expression levels. Using ribosome profiling, we identified robust changes in the translational kinetics of the two variants and were able to identify a region in the gene that may have a role in altering the conformation of the protein. Our data have direct implications for codon optimization strategies, for production of recombinant proteins and gene therapies.