bluuebunny/crossref_metadata_2025 huggingface dataset:
Response Bias in Survey Measures of Voter Behavior: Implications for Measurement and Inference
Authors: Adida Claire , Gottlieb Jessica , Kramon Eric , McClendon Gwyneth
Published: March 2019

This short report exploits a unique opportunity to investigate the implications of response bias in survey questions about voter turnout and vote choice in new democracies. We analyze data from a field experiment in Benin, where we gathered official election results and panel survey data representative at the village level, allowing us to directly compare average outcomes across both measurement instruments in a large number of units. We show that survey respondents consistently overreport turning out to vote and voting for the incumbent, and that the bias is large and worse in contexts where question sensitivity is higher. This has important implications for the inferences we draw about an experimental treatment, indicating that the response bias we identify is correlated with treatment. Although the results using the survey data suggest that the treatment had the hypothesized impact, they are also consistent with social desirability bias. By contrast, the administrative data lead to the conclusion that the treatment had no effect.
Annatto (Bixa orellana) δ-TCT supplementation protected against embryonic DNA damages through alterations in PI3K/ Akt-Cyclin D1 pathway
Authors: Mutalip Siti Syairah Mohd , Rajikin Mohd Hamim , Rahim Sharaniza Ab , Khan Norashikin Mohamed Noor
Published: March 2019

Abstract. Protective action by annatto-derived delta-tocotrienol (δ-TCT) and soy-derived alpha-tocopherol (α-TOC) through the regulation of PI3K/Akt-Cyclin D1 pathway against the nicotine-induced DNA damages is the focus of the present study. Nicotine, which has been widely reported to have numerous adverse effects on the reproductive system, was used as reproductive toxicant. 48 female balb/c mice (6–8 weeks) (23–25 g) were randomly divided into 8 groups (G1-G8; n = 6) and treated with either nicotine or/and annatto δ-TCT/soy α-TOC for 7 consecutive days. On Day 8, the females were superovulated and mated before euthanized for embryo collection (46 hours post-coitum). Fifty 2-cell embryos from each group were used in gene expression analysis using Affymetrix QuantiGene Plex2.0 assay. Findings indicated that nicotine (G2) significantly decreased (p < 0.05) the number of produced 2-cell embryos compared to control (G1). Intervention with mixed annatto δ-TCT (G3) and pure annatto δ-TCT (G4) significantly increased the number of produced 2-cell embryos by 127 % and 79 % respectively compared to G2, but these were lower than G1. Concurrent treatment with soy α-TOC (G5) decreased embryo production by 7 %. Supplementations with δ-TCT and α-TOC alone (G6-G8) significantly increased (p < 0.05) the number of produced 2-cell embryos by 50 %, 36 % and 41 % respectively, compared to control (G1). These results were found to be associated with the alterations in the PI3K/Akt-Cyclin D1 gene expressions, indicating the inhibitory effects of annatto δ-TCT and soy α-TOC against the nicotinic embryonic damages. To our knowledge, this is the first attempt on studying the benefits of annatto δ-TCT on murine preimplantation 2-cell embryos.
Cross-Lagged Relationships Between Self-Esteem, Self-Construal, and Happiness in a Three-Wave Longitudinal Study
Authors: Moza Daniela , Maricuțoiu Laurențiu , Gavreliuc Alin
Published: March 2019

Abstract. Previous research established that an independent construal of the self is associated with higher self-esteem, which, in turn, is associated with increased happiness. Regarding the directionality of these relationships, theoretical arguments have suggested that self-construal precedes self-esteem and that self-esteem precedes happiness. However, most research in this area is cross-sectional, thus limiting any conclusions about directionality. The present study tested these relationships in 101 Romanian undergraduates using a 3-wave cross-lagged design with a 6-month time lag between every two waves. Structural equation modeling analyses revealed that self-esteem is an antecedent of both happiness and dimensions of independent self-construal (i.e., consistency vs. variability and self-expression vs. harmony). In other words, one’s positive evaluation of self-worth precedes one’s self-perception as being a happy and independent person. The findings are discussed with respect to the theoretical and practical implications, along with limitations and suggestions for future research.
Quantifying Observational Errors in Biogeochemical‐Argo Oxygen, Nitrate, and Chlorophyll a Concentrations
Authors: Mignot A. , D'Ortenzio F. , Taillandier V. , Cossarini G. , Salon S.
Published: March 2019

Biogeochemical (BGC)‐Argo floats observations are becoming a major data source for assimilation into and constraining of ocean biogeochemical models. An important prerequisite for a successful synthesis between models and observations is the characterization of the observational errors in BGC‐Argo float data. The root‐mean‐square error and multiplicative and additive biases in quality‐controlled data sets of oxygen, nitrate, and chlorophyll a concentrations collected with 17 BGC‐Argo floats in the Mediterranean Sea between 2013 and 2017 are assessed using the triple collocation analysis. The analysis suggests that BGC‐Argo float oxygen, nitrate and chlorophyll a concentrations data have an additive bias of 2.9 ± 5.5 μmol/kg, 0.46 ± 0.07 μmol/kg, and −0.06 ± 0.02 mg/m3, respectively. The root‐mean‐square error is evaluated at 5.1 ± 0.8 μmol/kg, 0.25 ± 0.07 μmol/kg, and 0.03 ± 0.01 mg/m3. Additional studies should determine whether these values are applicable to the global ocean.
Earthquake‐Related Structures Beneath the Southernmost Portion of the Ryukyu Arc and Forearc
Authors: Wang Shiou‐Ya , Hsu Shu‐Kun , Yeh Yi‐Ching
Published: March 2019

Moderate to large earthquakes repeatedly occur beneath the southernmost Ryukyu arc and forearc, but the seismogenic structures were poorly studied. To better understand the southernmost Ryukyu seismogenic structures, we have deployed ocean bottom seismometers to record the aftershocks of a large earthquake in 2015. As a result, several groups of aftershocks are associated with the seismogenic structures. A deep group coincides with the north‐dipping seismogenic zone that terminates near the tip of the mantle wedge beneath the Ryukyu Arc. A shallow group dips southward from the southern slope of the Ryukyu Arc to the southern end of the aftershocks; this group shows south‐dipping normal faulting character and accompanies the lower crust exhumation of Ryukyu Arc above the seismogenic zone. A plate interface step‐down beneath the seismogenic zone is inferred. A crustal underplating and exhumation around the seismogenic zone have taken place synchronously during the earthquake event.
MMP9/RAGE pathway overactivation mediates redox dysregulation and neuroinflammation, leading to inhibitory/excitatory imbalance: a reverse translation study in schizophrenia patients
Authors: Dwir Daniella , Giangreco Basilio , Xin Lijing , Tenenbaum Liliane , Cabungcal Jan-Harry , Steullet Pascal , Goupil Audrey , Cleusix Martine , Jenni Raoul , Chtarto Abdelwahed , Baumann Philipp S. , Klauser Paul , Conus Philippe , Tirouvanziam Rabindra , Cuenod Michel , Do Kim Q.
Published: March 2019

Various mechanisms involved in schizophrenia pathophysiology, such as dopamine dysregulation, glutamate/NMDA receptor dysfunction, neuroinflammation or redox imbalance, all appear to converge towards an oxidative stress “hub” affecting parvalbumine interneurones (PVI) and their perineuronal nets (PNN) (Lancet Psychiatry. 2015;2:258–70); (Nat Rev Neurosci. 2016;17:125–34). We aim to investigate underlying mechanisms linking oxidative stress with neuroinflammatory and their long-lasting harmful consequences. In a transgenic mouse of redox dysregulation carrying a permanent deficit of glutathione synthesis (gclm−/−), the anterior cingulate cortex presented early in the development increased oxidative stress which was prevented by the antioxidant N-acetylcysteine (Eur J Neurosci. 2000;12:3721–8). This oxidative stress induced microglia activation and redox-sensitive matrix metalloproteinase 9 (MMP9) stimulation, leading to the receptor for advanced glycation end-products (RAGE) shedding into soluble and nuclear forms, and subsequently to nuclear factor-kB (NF-kB) activation and secretion of various cytokines. Blocking MMP9 activation prevented this sequence of alterations and rescued the normal maturation of PVI/PNN, even if performed after an additional insult that exacerbated the long term PVI/PNN impairments. MMP9 inhibition thus appears to be able to interrupt the vicious circle that maintains the long-lasting deleterious effects of the reciprocal interaction between oxidative stress and neuroinflammation, impacting on PVI/PNN integrity. Translation of these experimental findings to first episode patients revealed an increase in plasma soluble RAGE relative to healthy controls. This increase was associated with low prefrontal GABA levels, potentially predicting a central inhibitory/excitatory imbalance linked to RAGE shedding. This study paves the way for mechanistically related biomarkers needed for early intervention and MMP9/RAGE pathway modulation may lead to promising drug targets.
Untangling hidden nutrient dynamics: rapid ammonium cycling and single-cell ammonium assimilation in marine plankton communities
Authors: Klawonn Isabell , Bonaglia Stefano , Whitehouse Martin J , Littmann Sten , Tienken Daniela , Kuypers Marcel M M , Brüchert Volker , Ploug Helle
Published: March 2019

Ammonium is a central nutrient in aquatic systems. Yet, cell-specific ammonium assimilation among diverse functional plankton is poorly documented in field communities. Combining stable-isotope incubations (15N-ammonium, 15N2 and 13C-bicarbonate) with secondary-ion mass spectrometry, we quantified bulk ammonium dynamics, N2-fixation and carbon (C) fixation, as well as single-cell ammonium assimilation and C-fixation within plankton communities in nitrogen (N)-depleted surface waters during summer in the Baltic Sea. Ammonium production resulted from regenerated (≥91%) and new production (N2-fixation, ≤9%), supporting primary production by 78–97 and 2–16%, respectively. Ammonium was produced and consumed at balanced rates, and rapidly recycled within 1 h, as shown previously, facilitating an efficient ammonium transfer within plankton communities. N2-fixing cyanobacteria poorly assimilated ammonium, whereas heterotrophic bacteria and picocyanobacteria accounted for its highest consumption (~20 and ~20–40%, respectively). Surprisingly, ammonium assimilation and C-fixation were similarly fast for picocyanobacteria (non-N2-fixing Synechococcus) and large diatoms (Chaetoceros). Yet, the population biomass was high for Synechococcus but low for Chaetoceros. Hence, autotrophic picocyanobacteria and heterotrophic bacteria, with their high single-cell assimilation rates and dominating population biomass, competed for the same nutrient source and drove rapid ammonium dynamics in N-depleted marine waters.
BAG3 promotes autophagy and glutaminolysis via stabilizing glutaminase
Authors: Zhao Song , Wang Jia-Mei , Yan Jing , Zhang Da-Lin , Liu Bao-Qin , Jiang Jing-Yi , Li Chao , Li Si , Meng Xiao-Na , Wang Hua-Qin
Published: March 2019

Bcl-2 associated athanogene 3 (BAG3) is an important molecule that maintains oncogenic features of cancer cells via diverse mechanisms. One of the important functions assigned to BAG3 is implicated in selective macroautophagy/autophagy, which attracts much attention recently. However, the mechanism underlying regulation of autophagy by BAG3 has not been well defined. Here, we describe that BAG3 enhances autophagy via promotion of glutamine consumption and glutaminolysis. Glutaminolysis initiates with deamination of glutamine by glutaminase (GLS), by which yields glutamate and ammonia in mitochondria. The current study demonstrates that BAG3 stabilizes GLS via prohibition its interaction with SIRT5, thereby hindering its desuccinylation at Lys158 and Lys164 sites. As an underlying molecular mechanism, we demonstrate that BAG3 interacts with GLS and decreases SIRT5 expression. The current study also demonstrates that occupation by succinyl at Lys158 and Lys164 sites prohibits its Lys48-linked ubiquitination, thereby preventing its subsequent proteasomal degradation. Collectively, the current study demonstrates that BAG3 enhances autophagy via stabilizing GLS and promoting glutaminolysis. For the first time, this study reports that succinylation competes with ubiquitination to regulate proteasomal GLS degradation.
Long non-coding RNA Taurine upregulated gene 1 promotes osteosarcoma cell metastasis by mediating HIF-1α via miR-143-5p
Authors: Yu Xiao , Hu Lei , Li Suoyuan , Shen Jun , Wang Donglai , Xu Renjie , Yang Huilin
Published: March 2019

Early aggressive metastasis of osteosarcoma (OS) leads to rapid progression and poor prognosis. Increasing evidence has demonstrated that long non-coding RNAs (lncRNAs) could serve as crucial regulators to modulate tumour metastasis. In this study, we reported the critical role of lncRNA TUG1 in determining OS metastasis. TUG1 was significantly upregulated in OS tissues and associated with tumour size, distant metastasis, TNM stage, and overall and recurrence-free survival, which further indicated poor prognosis. Furthermore, CAFs-derived TGF-β could upregulate TUG1 expression, and the crosstalk between CAFs and OS cells induced TUG1 to promote OS cell metastasis. Dysregulated TUG1 expression could act as an miRNA “sponge” to competitively protect the HIF-1α mRNA 3′UTR from miR-143-5p. Our study emphasised the effects of TUG1 in OS and demonstrated a novel axis by which TUG1 regulated OS cell metastasis, angiogenesis, and proliferation in vivo and in vitro. Collectively, TUG1 might be a prognostic indicator for OS and could be a therapeutic target for OS.
TAZ sensitizes EGFR wild-type non-small-cell lung cancer to gefitinib by promoting amphiregulin transcription
Authors: Yuan Weiwei , Xu Wei , Li Yan , Jiang Wei , Li Yue , Huang Qiqing , Chen Bo , Wu Shuangshuang , Wang Yu , Song Weiwei , Zhao Weihong , Wu Jianqing
Published: March 2019

Comparatively less toxic and more tolerated, epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) are recommendable for advanced non-small-cell lung cancer (NSCLC) patients with EGFR-sensitive mutations. Some EGFR wild-type patients with specific biomarkers also show a response to the drug. TAZ is an oncogene closely associated with the therapeutic effect of EGFR-TKIs. However, this association remains to be clarified. This study aimed to clarify the mechanism through which TAZ sensitizes EGFR wild-type NSCLC to gefitinib. We used CCK-8 assays and in vivo experiments to investigate the influence of TAZ on gefitinib in EGFR wild-type NSCLC. To further validate the tumorigenic role of TAZ, we performed Human umbilical vein endothelial cell (HUVEC) tube formation and migration assays. Luciferase reporter assays, quantitative real-time PCR (qPCR), immunoblotting and Chromatin immunoprecipitation collaborated with qPCR illuminated the mechanism through which TAZ caused those phenotypes. The results showed TAZ promoted the angiogenesis of NSCLC cell lines and improved gefitinib sensitivity in EGFR wild-type NSCLC in vitro and in vivo. Luciferase reporter assays and ChIP-qPCR experiments showed TAZ upregulated AREG by promoting its transcription. EGFR signaling pathway was activated as TAZ was highly expressed. Rescue experiments were conducted to confirm the indispensable role of AREG in tumorigenesis and gefitinib sensitivity regulated by TAZ. Our study concluded that TAZ sensitized EGFR wild-type NSCLC to gefitinib through promoting amphiregulin transcription.
Discontinuous rate-stiffening in a granular composite modeled after cornstarch and water
Authors: Chen David Z. , Zheng Hu , Wang Dong , Behringer Robert P.
Published: March 2019

Cornstarch in water exhibits impact-activated solidification (IAS) and strong discontinuous shear thickening, with “shear jamming”. However, these phenomena are absent in cornstarch in ethanol. Here we show that cornstarch granules swell under ambient conditions. We postulate that this granule swelling is linked to an interparticle force scale that introduces a discontinuous rate-dependence to the generation of stable contacts between granules. We studied this force scale by coating sand with ~ 2 μm-thick polydimethysiloxane, creating a material that exhibits a similar IAS and discontinuous deformation rate-stiffening despite being a granular composite, not a suspension. This result suggests rate-dependence can be tuned by coating granular materials, introducing an interparticle force scale from rate-dependent properties present in the coating material. Our work provides insights into the unique behavior of cornstarch in water, bridges our understanding of suspensions and dry granular materials, and introduces a method to make discontinuous rate-dependent materials without suspending particles.
Characterization of an HPV33 natural variant with enhanced transcriptional activity suggests a role for C/EBPβ in the regulation of the viral early promoter
Authors: Alvarez Jennifer , Gagnon David , Coutlée François , Archambault Jacques
Published: March 2019

The Long Control Region (LCR) of the human papillomavirus (HPV) genome encompasses the early promoter (EP) that drives expression of the viral oncogenes in infected cells and HPV-associated cancers. Here, we report on a natural variant of HPV33 that displays higher EP activity than the prototype in transfected C33A and HeLa cervical carcinoma cells, and in the osteosarcoma U2OS cell line which supports replication of HPV episomes. This increased promoter activity was ascribed to a single nucleotide variation in the LCR, T7791C, in a putative binding site for the transcription factor C/EBPβ. T7791C abrogated binding of recombinant C/EBPβ to this site in vitro and stimulated the EP in vivo, suggesting that it abrogates a negatively-acting regulatory element. A second C/EBPβ binding site was identified in vitro that activated the EP in vivo and whose function and location in the epithelial-specific enhancer is shown to be conserved in the highly prevalent HPV18. These results suggest that C/EBPβ is both an activator and a repressor of the HPV33 EP, acting via two distinct binding sites. Prediction of C/EBPβ sites in the LCR of 186 HPV types suggests that C/EBPβ regulation of the EP is common among high‐risk viruses from the α genus.
Combining magnetic forces for contactless manipulation of fluids in microelectrode-microfluidic systems
Authors: Haehnel Veronika , Khan Foysal Z. , Mutschke Gerd , Cierpka Christian , Uhlemann Margitta , Fritsch Ingrid
Published: March 2019

A novel method to drive and manipulate fluid in a contactless way in a microelectrode-microfluidic system is demonstrated by combining the Lorentz and magnetic field gradient forces. The method is based on the redox-reaction [Fe(CN)6]3−/[Fe(CN)6]4− performed in a magnetic field oriented perpendicular to the ionic current that crosses the gap between two arrays of oppositely polarized microelectrodes, generating a magnetohydrodynamic flow. Additionally, a movable magnetized CoFe micro-strip is placed at different positions beneath the gap. In this region, the magnetic flux density is changed locally and a strong magnetic field gradient is formed. The redox-reaction changes the magnetic susceptibility of the electrolyte near the electrodes, and the resulting magnetic field gradient exerts a force on the fluid, which leads to a deflection of the Lorentz force-driven main flow. Particle Image Velocity measurements and numerical simulations demonstrate that by combining the two magnetic forces, the flow is not only redirected, but also a local change of concentration of paramagnetic species is realized.
Effects of Intradermal Radiofrequency Treatment and Intense Pulsed Light Therapy in an Acne-induced Rabbit Ear Model
Authors: Seok Joon , Kim Jong Hwan , Kim Jae Min , Kwon Tae Rin , Choi Sun Young , Li Kapsok , Kim Beom Joon
Published: March 2019

Acne vulgaris is a common condition that can have psychologically deleterious effects. Since current treatments carry the risks of antibiotic resistance or teratogenicity, novel treatment modalities are under investigation. Our study investigated the efficacy of intradermal radiofrequency treatment (RF) and intense pulsed light (IPL) in the treatment of acne vulgaris in a rabbit ear model. We evaluated the effectiveness of IPL, RF, and a combination treatment on cultured Cuticobacterium acnes strains in an induced rabbit ear model, according to clinical outcomes as well as histological and immunological approaches. We found that RF treatment markedly decreases papule volume, while IPL appears to have an immunomodulatory effect. In combination, the two have an additive effect in treatment. These findings suggest that combination of RF and IPL may be an effective therapeutic option for the treatment of acne vulgaris.
Formation processes for large ejecta and interactions with melt pool formation in powder bed fusion additive manufacturing
Authors: Nassar Abdalla R. , Gundermann Molly A. , Reutzel Edward W. , Guerrier Paul , Krane Michael H. , Weldon Matthew J.
Published: March 2019

Ejecta with a size much larger than the mean particle size of feedstock powder have been observed in powder bed fusion additive manufacturing, both during post-process sieving and embedded within built components. However, their origin has not been adequately explained. Here, we test a hypothesis on the origin of large (much larger than the mass-median-diameter of feedstock powder) ejecta—that, in part, they result from stochastic, inelastic collisions of ejecta and coalescence of partially-sintered agglomerates. The hypothesis is tested using direct observation of ejecta behavior, via high-speed imaging, to identify interactions between ejecta and consequences on melt pool formation. We show that stochastic collisions occur both between particles which are nearly-simultaneously expelled from the laser interaction zone and between particles ejected from distant locations. Ejecta are also shown to perturb melt pool geometry, which is argued to be a potential cause of lack-of-fusion flaws.
Pore-forming protein complexes from Pleurotus mushrooms kill western corn rootworm and Colorado potato beetle through targeting membrane ceramide phosphoethanolamine
Authors: Panevska Anastasija , Hodnik Vesna , Skočaj Matej , Novak Maruša , Modic Špela , Pavlic Ivana , Podržaj Sara , Zarić Miki , Resnik Nataša , Maček Peter , Veranič Peter , Razinger Jaka , Sepčić Kristina
Published: March 2019

Aegerolysins ostreolysin A (OlyA) and pleurotolysin A (PlyA), and pleurotolysin B (PlyB) with the membrane-attack-complex/perforin domain are proteins from the mushroom genusPleurotus. Upon binding to sphingomyelin/cholesterol-enriched membranes, OlyA and PlyA can recruit PlyB to form multimeric bi-component transmembrane pores. Recently,Pleurotusaegerolysins OlyA, PlyA2 and erylysin A (EryA) were demonstrated to preferentially bind to artificial lipid membranes containing 50 mol% ceramide phosphoethanolamine (CPE), the main sphingolipid in invertebrate cell membranes. In this study, we demonstrate that OlyA6, PlyA2 and EryA bind to insect cells and to artificial lipid membranes with physiologically relevant CPE concentrations. Moreover, these aegerolysins permeabilize these membranes when combined with PlyB. These aegerolysin/PlyB complexes show selective toxicity toward western corn rootworm larvae and adults and Colorado potato beetle larvae. These data strongly suggest that these aegerolysin/PlyB complexes recognize CPE as their receptor molecule in the insect midgut. This mode of binding is different from those described for similar aegerolysin-based bacterial complexes, or otherBacillus thuringiensisCry toxins, which have protein receptors. Targeting ofPleurotusaegerolysins to CPE and formation of transmembrane pores in concert with PlyB suggest the use of aegerolysin/PlyB complexes as novel biopesticides for the control of western corn rootworm and Colorado potato beetle.
Novel compound mutations in the mitochondrial translation elongation factor (TSFM) gene cause severe cardiomyopathy with myocardial fibro-adipose replacement
Authors: Perli Elena , Pisano Annalinda , Glasgow Ruth I. C. , Carbo Miriam , Hardy Steven A. , Falkous Gavin , He Langping , Cerbelli Bruna , Pignataro Maria Gemma , Zacara Elisabetta , Re Federica , Della Monica Paola Lilla , Morea Veronica , Bonnen Penelope E. , Taylor Robert W. , d’Amati Giulia , Giordano Carla
Published: March 2019

Primary mitochondrial dysfunction is an under-appreciated cause of cardiomyopathy, especially when cardiac symptoms are the unique or prevalent manifestation of disease. Here, we report an unusual presentation of mitochondrial cardiomyopathy, with dilated phenotype and pathologic evidence of biventricular fibro-adipose replacement, in a 33-year old woman who underwent cardiac transplant. Whole exome sequencing revealed two novel compound heterozygous variants in the TSFM gene, coding for the mitochondrial translation elongation factor EF-Ts. This protein participates in the elongation step of mitochondrial translation by binding and stabilizing the translation elongation factor Tu (EF-Tu). Bioinformatics analysis predicted a destabilization of the EF-Ts variants complex with EF-Tu, in agreement with the dramatic steady-state level reduction of both proteins in the clinically affected myocardium, which demonstrated a combined respiratory chain enzyme deficiency. In patient fibroblasts, the decrease of EF-Ts was paralleled by up-regulation of EF-Tu and induction of genes involved in mitochondrial biogenesis, along with increased expression of respiratory chain subunits and normal oxygen consumption rate. Our report extends the current picture of morphologic phenotypes associated with mitochondrial cardiomyopathies and confirms the heart as a main target of TSFM dysfunction. The compensatory response detected in patient fibroblasts might explain the tissue-specific expression of TSFM-associated disease.
Position 123 of halohydrin dehalogenase HheG plays an important role in stability, activity, and enantioselectivity
Authors: Solarczek Jennifer , Klünemann Thomas , Brandt Felix , Schrepfer Patrick , Wolter Mario , Jacob Christoph R. , Blankenfeldt Wulf , Schallmey Anett
Published: March 2019

HheG from Ilumatobacter coccineus is a halohydrin dehalogenase with synthetically useful activity in the ring opening of cyclic epoxides with various small anionic nucleophiles. This enzyme provides access to chiral β-substituted alcohols that serve as building blocks in the pharmaceutical industry. Wild-type HheG suffers from low thermostability, which poses a significant drawback for potential applications. In an attempt to thermostabilize HheG by protein engineering, several single mutants at position 123 were identified which displayed up to 14 °C increased apparent melting temperatures and up to three-fold higher activity. Aromatic amino acids at position 123 resulted even in a slightly higher enantioselectivity. Crystal structures of variants T123W and T123G revealed a flexible loop opposite to amino acid 123. In variant T123G, this loop adopted two different positions resulting in an open or partially closed active site. Classical molecular dynamics simulations confirmed a high mobility of this loop. Moreover, in variant T123G this loop adopted a position much closer to residue 123 resulting in denser packing and increased buried surface area. Our results indicate an important role for position 123 in HheG and give first structural and mechanistic insight into the thermostabilizing effect of mutations T123W and T123G.
Automatic diagnosis of neurological diseases using MEG signals with a deep neural network
Authors: Aoe Jo , Fukuma Ryohei , Yanagisawa Takufumi , Harada Tatsuya , Tanaka Masataka , Kobayashi Maki , Inoue You , Yamamoto Shota , Ohnishi Yuichiro , Kishima Haruhiko
Published: March 2019

The application of deep learning to neuroimaging big data will help develop computer-aided diagnosis of neurological diseases. Pattern recognition using deep learning can extract features of neuroimaging signals unique to various neurological diseases, leading to better diagnoses. In this study, we developed MNet, a novel deep neural network to classify multiple neurological diseases using resting-state magnetoencephalography (MEG) signals. We used the MEG signals of 67 healthy subjects, 26 patients with spinal cord injury, and 140 patients with epilepsy to train and test the network using 10-fold cross-validation. The trained MNet succeeded in classifying the healthy subjects and those with the two neurological diseases with an accuracy of 70.7 ± 10.6%, which significantly exceeded the accuracy of 63.4 ± 12.7% calculated from relative powers of six frequency bands (δ: 1–4 Hz; θ: 4–8 Hz; low-α: 8–10 Hz; high-α: 10–13 Hz; β: 13–30 Hz; low-γ: 30–50 Hz) for each channel using a support vector machine as a classifier (p = 4.2 × 10−2). The specificity of classification for each disease ranged from 86–94%. Our results suggest that this technique would be useful for developing a classifier that will improve neurological diagnoses and allow high specificity in identifying diseases.
A new common functional coding variant at the DDC gene change renal enzyme activity and modify renal dopamine function
Authors: Miramontes-Gonzalez Jose Pablo , Hightower C. Makena , Zhang Kuixing , Kurosaki Hiroki , Schork Andrew J. , Biswas Nilima , Vaingankar Sucheta , Mahata Manjula , Lipkowitz Michael S. , Nievergelt Caroline M. , Baker Dewleen G. , Ziegler Michael G. , León-Jiménez David , González-Sarmiento Rogelio , Ichinose Hiroshi , O’Connor Daniel T.
Published: March 2019

The intra-renal dopamine (DA) system is highly expressed in the proximal tubule and contributes to Na+ and blood pressure homeostasis, as well as to the development of nephropathy. In the kidney, the enzyme DOPA Decarboxylase (DDC) originating from the circulation. We used a twin/family study design, followed by polymorphism association analysis at DDC locus to elucidate heritable influences on renal DA production. Dense single nucleotide polymorphism (SNP) genotyping across the DDC locus on chromosome 7p12 was analyzed by re-sequencing guided by trait-associated genetic markers to discover the responsible genetic variation. We also characterized kinetics of the expressed DDC mutant enzyme. Systematic polymorphism screening across the 15-Exon DDC locus revealed a single coding variant in Exon-14 that was associated with DA excretion and multiple other renal traits indicating pleiotropy. When expressed and characterized in eukaryotic cells, the 462Gln variant displayed lower Vmax (maximal rate of product formation by an enzyme) (21.3 versus 44.9 nmol/min/mg) and lower Km (substrate concentration at which half-maximal product formation is achieved by an enzyme.)(36.2 versus 46.8 μM) than the wild-type (Arg462) allele. The highly heritable DA excretion trait is substantially influenced by a previously uncharacterized common coding variant (Arg462Gln) at the DDC gene that affects multiple renal tubular and glomerular traits, and predicts accelerated functional decline in chronic kidney disease.
Vascular Response to Sildenafil Citrate in Aging and Age-Related Macular Degeneration
Authors: Yiu Glenn , Vuong Vivian S. , Tran Steven , Migacz Justin , Cunefare David , Farsiu Sina , Khandelwal Neha , Agrawal Rupesh , Cheung Chui Ming Gemmy
Published: March 2019

Age-related macular degeneration (AMD) - the leading cause of vision loss in the elderly - share many risks factors as atherosclerosis, which exhibits loss of vascular compliance resulting from aging and oxidative stress. Here, we attempt to explore choroidal and retinal vascular compliance in patients with AMD by evaluating dynamic vascular changes using live ocular imaging following treatment with oral sildenafil citrate, a phosphodiesterase type 5 (PDE5) inhibitor and potent vasodilator. Enhanced-depth imaging optical coherence tomography (EDI-OCT) and OCT angiography (OCT-A) were performed on 46 eyes of 23 subjects, including 15 patients with non-exudative AMD in one eye and exudative AMD in the fellow eye, and 8 age-matched control subjects. Choroidal thickness, choroidal vascularity, and retinal vessel density were measured across the central macula at 1 and 3 hours after a 100 mg oral dose of sildenafil citrate. Baseline choroidal thickness was 172.1 ± 60.0 μm in non-exudative AMD eyes, 196.4 ± 89.8 μm in exudative AMD eyes, and 207.4 ± 77.7 μm in control eyes, with no difference between the 3 groups (P = 0.116). After sildenafil, choroidal thickness increased by 6.0% to 9.0% at 1 and 3 hours in all groups (P = 0.001–0.014). Eyes from older subjects were associated with choroidal thinning at baseline (P = 0.005) and showed less choroidal expansion at 1 hour and 3 hours after sildenafil (P = 0.001) regardless of AMD status (P = 0.666). The choroidal thickening appeared to be primarily attributed to expansion of the stroma rather than luminal component. Retinal vascular density remained unchanged after sildenafil in all 3 groups (P = 0.281–0.587). Together, our studies suggest that vascular response of the choroid to sildenafil decreases with age, but is not affected by the presence of non-exudative or exudative AMD, providing insight into changes in vessel compliance in aging and AMD.
Minimally-verbal children with autism show deficits in theta and gamma oscillations during processing of semantically-related visual information
Authors: Ortiz-Mantilla Silvia , Cantiani Chiara , Shafer Valerie L. , Benasich April A.
Published: March 2019

To acquire language, children must build phonemic representations of their native language, learn to associate auditory words to visual objects and assemble a lexicon. It is not clear however, whether the limited linguistic ability seen in minimally-verbal (MV) children with Autism Spectrum Disorder (ASD) relates to deficits in cortical representation of an object and/or in linking an object to its semantic information. This EEG-based study investigated neural mechanisms underlying visual processing of common objects in MV-ASD and control children. Ten MV-ASD children, 4- to 7- years-old and 15 age/gender-matched controls, were presented with a picture-word matching paradigm. Time-frequency analyses were conducted at the sources generating the event-related responses at both early and late visual processing. Permutation testing identified spectral power and phase coherence clusters that significantly differed between the groups. As compared to controls, MV-ASD children exhibited smaller amplitudes and longer source latencies; decreased gamma and theta power with less theta phase coherence in occipital regions, and reduced frontal gamma power. Our results confirm that visual processing is altered in MV-ASD children and suggest that some of the linguistic differences observed in these children arise from impaired object/label cortical representations and reduced allocation of attention, which would impact lexical acquisition.
Frequency-specific coupling in fronto-parieto-occipital cortical circuits underlie active tactile discrimination
Authors: Kunicki Carolina , C. Moioli Renan , Pais-Vieira Miguel , Salles Cunha Peres André , Morya Edgard , A. L. Nicolelis Miguel
Published: March 2019

Processing of tactile sensory information in rodents is critically dependent on the communication between the primary somatosensory cortex (S1) and higher-order integrative cortical areas. Here, we have simultaneously characterized single-unit activity and local field potential (LFP) dynamics in the S1, primary visual cortex (V1), anterior cingulate cortex (ACC), posterior parietal cortex (PPC), while freely moving rats performed an active tactile discrimination task. Simultaneous single unit recordings from all these cortical regions revealed statistically significant neuronal firing rate modulations during all task phases (anticipatory, discrimination, response, and reward). Meanwhile, phase analysis of pairwise LFP recordings revealed the occurrence of long-range synchronization across the sampled fronto-parieto-occipital cortical areas during tactile sampling. Causal analysis of the same pairwise recorded LFPs demonstrated the occurrence of complex dynamic interactions between cortical areas throughout the fronto-parietal-occipital loop. These interactions changed significantly between cortical regions as a function of frequencies (i.e. beta, theta and gamma) and according to the different phases of the behavioral task. Overall, these findings indicate that active tactile discrimination by rats is characterized by much more widespread and dynamic complex interactions within the fronto-parieto-occipital cortex than previously anticipated.
An oligonucleotide synthesizer based on a microreactor chip and an inkjet printer
Authors: Li Hui , Huang Ye , Wei Zewen , Wang Wei , Yang Zhenjun , Liang Zicai , Li Zhihong
Published: March 2019

Synthetic oligonucleotides (oligos) are important tools in the fields of molecular biology and genetic engineering. For applications requiring a large number of oligos with high concentration, it is critical to perform high throughput oligo synthesis and achieve high yield of each oligo. This study reports a microreactor chip for oligo synthesis. By incorporating silica beads in the microreactors, the surface area of the solid substrate for oligo synthesis increases significantly in each microreactor. These beads are fixed in the microreactors to withstand the flushing step in oligo synthesis. Compared to conventional synthesis methods, this design is able to avoid protocols to hold the beads and integrate more microreactors on a chip. An inkjet printer is utilized to deliver chemical reagents in the microreactors. To evaluate the feasibility of oligo synthesis using this proof-of-concept synthesizer, an oligo with six nucleotide units is successfully synthesized.
Enhancing entanglement detection of quantum optical frequency combs via stimulated emission
Authors: Arkhipov Ievgen I. , Yoon Tai Hyun , Miranowicz Adam
Published: March 2019

We investigate the performance of a certain nonclassicality identifier, expressed via integrated second-order intensity moments of optical fields, in revealing bipartite entanglement of quantum-optical frequency combs (QOFCs), which are generated in both spontaneous and stimulated parametric down-conversion processes. We show that, by utilizing that nonclassicality identifier, one can well identify the entanglement of the QOFC directly from the experimentally measured intensity moments without invoking any state reconstruction techniques or homodyne detection. Moreover, we demonstrate that the stimulated generation of the QOFC improves the entanglement detection of these fields with the nonclassicality identifier. Additionally, we show that the nonclassicality identifier can be expressed in a factorized form of detectors quantum efficiencies and the number of modes, if the QOFC consists of many copies of the same two-mode twin beam. As an example, we apply the nonclassicality identifier to two specific types of QOFC, where: (i) the QOFC consists of many independent two-mode twin beams with non-overlapped spatial frequency modes, and (ii) the QOFC contains entangled spatial frequency modes which are completely overlapped, i.e., each mode is entangled with all the remaining modes in the system. We show that, in both cases, the nonclassicality identifier can reveal bipartite entanglement of the QOFC including noise, and that it becomes even more sensitive for the stimulated processes.
Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome
Authors: Shin Seung Chul , Kim Hyun , Lee Jun Hyuck , Kim Han-Woo , Park Joonho , Choi Beom-Soon , Lee Sang-Choon , Kim Ji Hee , Lee Hyoungseok , Kim Sanghee
Published: March 2019

Parochlus steinenii is a winged midge from King George Island. It is cold-tolerant and endures the harsh Antarctic winter. Previously, we reported the genome of this midge, but the genome assembly with short reads had limited contig contiguity, which reduced the completeness of the genome assembly and the annotated gene sets. Recently, assembly contiguity has been increased using nanopore technology. A number of methods for enhancing the low base quality of the assembly have been reported, including long-read (e.g. Nanopolish) or short-read (e.g. Pilon) based methods. Based on these advances, we used nanopore technologies to upgrade the draft genome sequence of P. steinenii. The final assembled genome was 145,366,448 bases in length. The contig number decreased from 9,132 to 162, and the N50 contig size increased from 36,946 to 1,989,550 bases. The BUSCO completeness of the assembly increased from 87.8 to 98.7%. Improved assembly statistics helped predict more genes from the draft genome of P. steinenii. The completeness of the predicted gene model increased from 79.5 to 92.1%, but the numbers and types of the predicted repeats were similar to those observed in the short read assembly, with the exception of long interspersed nuclear elements. In the present study, we markedly improved the P. steinenii genome assembly statistics using nanopore sequencing, but found that genome polishing with high-quality reads was essential for improving genome annotation. The number of genes predicted and the lengths of the genes were greater than before, and nanopore technology readily improved genome information.
Targeting Modified Lipids during Routine Lipidomics Analysis using HILIC and C30 Reverse Phase Liquid Chromatography coupled to Mass Spectrometry
Authors: Pham Thu Huong , Zaeem Muhammad , Fillier Tiffany A. , Nadeem Muhammad , Vidal Natalia P. , Manful Charles , Cheema Sukhinder , Cheema Mumtaz , Thomas Raymond H.
Published: March 2019

Lipids are important biomolecules in all biological systems and serve numerous essential cellular functions. The global analysis of complex lipids is very challenging due to the extreme diversity in lipid structures. Variation in linkages and positions of fatty acyl chain(s) on the lipid backbone, functional group modification, occurrence of the molecular species as isomers or isobars are among some of the greatest challenges to resolve in lipidomics. In this work, we describe a routine analytical approach combining two liquid chromatography platforms: hydrophilic interaction (HILIC) and C30 reversed-phase chromatography (C30RP) coupled to high resolution mass spectrometry (HRMS) as complementary high throughput platforms to analyze complex lipid mixtures. Vascular plants (kale leaves and corn roots), rat brain and soil microbes were used as proxies to evaluate the efficiency of the enhanced approach to resolve traditional, as well as, modified lipids during routine lipidomics analysis. We report for the first time, the observation of a modified class of acylphosphatidylglycerol (acylPG) in corn roots by HILIC, and further resolution of the isomers using C30RP chromatography. We also used this approach to demonstrate the presence of high levels of N-monomethyl phosphatidylethanolamine (MMPE) in soil microbes, as well as to determine the regioisomers of lysophospholipids in kale leaves. Additionally, neutral lipids were demonstrated using C30RP chromatography in positive ion mode to resolve triacylglycerol isomers in rat brain. The work presented here demonstrates how the enhanced approach can more routinely permit novel biomarker discovery, or lipid metabolism in a wide range of biological samples.
The contribution of super typhoons to tropical cyclone activity in response to ENSO
Authors: Kang Nam-Young , Kim Dongjin , Elsner James B.
Published: March 2019

Western North Pacific tropical cyclone (TC) activity is known to have a significant response to El Niño and Southern Oscillation (ENSO). Among the TC intensity classifications, “super typhoon”, is widely used as a symbolic word for warning people about the potential for experiencing the most severe typhoon. This study quantifies the contribution of super typhoons to TC activity in response to ENSO, where the Southern Oscillation Index (SOI) is used to indicate the internal variation of ENSO. It is found that the number and the genesis location of non-super typhoons are little influenced by ENSO, and the changes are mostly by the addition of super typhoons. Historical levels of El Niño and La Niña span from −2σ to +2σ of the SOI. Over this range of SOI values, the mean response is 5.6 super typhoons (7.1 for El Niño and 1.5 for La Niña) which nearly matches the mean response overall of 6 storms (24.6 for El Niño and 18.6 for La Niña). The spatial distribution of TC genesis locations for different ENSO conditions does not completely explain these results.
Phenylpyrrole fungicides act on triosephosphate isomerase to induce methylglyoxal stress and alter hybrid histidine kinase activity
Authors: Brandhorst T. Tristan , Kean Iain R. L. , Lawry Stephanie M. , Wiesner Darin L. , Klein Bruce S.
Published: March 2019

Fludioxonil, a natural product of pyrrolnitrin, is a potent fungicide used on crops worldwide. Drug action requires the presence of a group III hybrid histidine kinase (HHK) and the high osmolarity glycerol (HOG) pathway. We have reported that the drug does not act directly on HHK, but triggers the conversion of the kinase to a phosphatase, which dephosphorylates Ypd1 to constitutively activate HOG signaling. Still, the direct drug target remains unknown and mode of action ill defined. Here, we heterologously expressed a group III HHK, dimorphism-regulating kinase 1 (Drk1) in Saccharomyces cerevisae to delineate fludioxonil’s target and action. We show that the drug interferes with triosephosphate isomerase (TPI) causing release of methylglyoxal (MG). MG activates the group III HHK and thus the HOG pathway. Drug action involved Drk1 cysteine 392, as a C392S substitution increased drug resistance in vivo. Drug sensitivity was reversed by dimedone treatment, indicating Drk1 responds in vivo to an aldehydic stress. Fludioxonil treatment triggered elevated cytosolic methylglyoxal. Likewise, methylglyoxal treatment of Drk1-expressing yeast phenocopied treatment with fludioxonil. Fludioxonil directly inhibited TPI and also caused it to release methylglyoxal in vitro. Thus, TPI is a drug target of the phenylpyrrole class of fungicides, inducing elevated MG which alters HHK activity, likely converting the kinase to a phosphatase that acts on Ypd1 to trigger HOG pathway activation and fungal cell death.
Temperature Chaos, Memory Effect, and Domain Fluctuations in the Spiral Antiferromagnet Dy
Authors: Kustov Sergey , Liubimova Iuliia , Corró Miguel , Torrens-Serra Joan , Wang Xiebin , Haines Charles R. S. , Salje Ekhard K. H.
Published: March 2019

The spiral antiferromagnetic phase of polycrystalline dysprosium between 140 K and the Néel temperature at 178 K and its domain wall (DW) dynamics were investigated using high-resolution ultrasonic spectroscopy. Two kinetic processes of quasi-static DW motion occur under non-isothermal and isothermal conditions. A “fast” process is proportional to the rate of the temperature change and results in a new category of anelastic phenomena: magnetic transient ultrasonic internal friction (IF). This IF, related to fast moving magnetic DWs, decays rapidly after interruptions of cooling/heating cycles. A second, “slow” kinetic process is seen as logarithmic IF relaxation under isothermal conditions. This second process is glass-like and results in memory and temperature chaos effects. Low-frequency thermal fluctuations of DWs, previously detected by X-ray photon correlation spectroscopy, are related to critical fluctuations with Brownian motion-like dynamics of DWs.