bluuebunny/crossref_metadata_2025 huggingface dataset:
The therapeutic significance of mutational signatures from DNA repair deficiency in cancer
Authors: Ma Jennifer , Setton Jeremy , Lee Nancy Y. , Riaz Nadeem , Powell Simon N.
Published: August 2018

Cancer is fundamentally a disease of the genome and inherited deficiencies in DNA repair pathways are well established to increase lifetime cancer risk. Computational analysis of pan-cancer data has identified signatures of mutational processes thought to be responsible for the pattern of mutations in any given cancer. These analyses identified altered DNA repair pathways in a much broader spectrum of cancers than previously appreciated with significant therapeutic implications. The development of DNA repair deficiency biomarkers is critical to the implementation of therapeutic targeting of repair-deficient tumors, using either DNA damaging agents or immunotherapy for the personalization of cancer therapy.
Sarcolab pilot study into skeletal muscle’s adaptation to long-term spaceflight
Authors: Rittweger Jörn , Albracht Kirsten , Flück Martin , Ruoss Severin , Brocca Lorenza , Longa Emanuela , Moriggi Manuela , Seynnes Olivier , Di Giulio Irene , Tenori Leonardo , Vignoli Alessia , Capri Miriam , Gelfi Cecilia , Luchinat Claudio , Franceschi Claudio , Bottinelli Roberto , Cerretelli Paolo , Narici Marco
Published: August 2018

Spaceflight causes muscle wasting. The Sarcolab pilot study investigated two astronauts with regards to plantar flexor muscle size, architecture, and function, and to the underlying molecular adaptations in order to further the understanding of muscular responses to spaceflight and exercise countermeasures. Two crew members (A and B) spent 6 months in space. Crew member A trained less vigorously than B. Postflight, A showed substantial decrements in plantar flexor volume, muscle architecture, in strength and in fiber contractility, which was strongly mitigated in B. The difference between these crew members closely reflected FAK-Y397 abundance, a molecular marker of muscle’s loading history. Moreover, crew member A showed downregulation of contractile proteins and enzymes of anaerobic metabolism, as well as of systemic markers of energy and protein metabolism. However, both crew members exhibited decrements in muscular aerobic metabolism and phosphate high energy transfer. We conclude that countermeasures can be effective, particularly when resistive forces are of sufficient magnitude. However, to fully prevent space-related muscular deterioration, intersubject variability must be understood, and intensive exercise countermeasures programs seem mandatory. Finally, proteomic and metabolomic analyses suggest that exercise benefits in space may go beyond mere maintenance of muscle mass, but rather extend to the level of organismic metabolism.
Post-class naps boost declarative learning in a naturalistic school setting
Authors: Cabral Thiago , Mota Natália B. , Fraga Lucia , Copelli Mauro , McDaniel Mark A. , Ribeiro Sidarta
Published: August 2018

Laboratory evidence of a positive effect of sleep on declarative memory consolidation suggests that naps can be used to boost school learning in a scalable, low-cost manner. The few direct investigations of this hypothesis have so far upheld it, but departed from the naturalistic setting by testing non-curricular contents presented by experimenters instead of teachers. Furthermore, nap and non-nap groups were composed of different children. Here we assessed the effect of post-class naps on the retention of Science and History curricular contents presented by the regular class teacher to 24 students from 5th grade. Retention was repeatedly measured 3–4 days after content learning, with weekly group randomization over 6 consecutive weeks. Contents followed by long naps (>30 min), but not short naps (<30 min), were significantly more retained than contents followed by waking (Cohen’s d = 0.7962). The results support the use of post-class morning naps to enhance formal education.
A new era in cytomegalovirus vaccinology: considerations for rational design of next-generation vaccines to prevent congenital cytomegalovirus infection
Authors: Nelson Cody S. , Herold Betsy C. , Permar Sallie R.
Published: August 2018

Human cytomegalovirus (HCMV), a member of the beta-herpesvirus family, is the most common cause of congenital infection worldwide as well as an important cause of morbidity in transplant recipients and immunosuppressed individuals. An estimated 1 in 150 infants are infected with HCMV at birth, which can result in lifelong, debilitating neurologic sequelae including microcephaly, sensorineural hearing loss, and cognitive impairment. Natural maternal immunity to HCMV decreases the frequency of reinfection and reduces risk of congenital transmission but does not completely protect against neonatal disease. Thus, a vaccine to reduce the incidence and severity of infant infection is a public health priority. A variety of candidate HCMV vaccine approaches have been tried previously, including live-attenuated viruses, glycoprotein subunit formulations, viral vectors, and single/bivalent DNA plasmids, but all have failed to reach target endpoints in clinical trials. Nevertheless, there is a great deal to be learned from the successes and failures of the HCMV vaccine field (both congenital and transplant-associated), as well as from vaccine development efforts for other herpesvirus pathogens including herpes simplex virus 1 and 2, varicella zoster virus, and Epstein–Barr virus. Here, we review those successes and failures, evaluating recent cutting-edge discoveries that have shaped the HCMV vaccine field and identifying topics of critical importance for future investigation. These considerations will inform rational design and evaluation of next-generation vaccines to prevent HCMV-associated congenital infection and disease.
In vitro and in vivo evaluation of the genotoxic and antigenotoxic potential of the major Chios mastic water constituents
Authors: Drosopoulou Elena , Vlastos Dimitris , Efthimiou Ioanna , Kyrizaki Paraskevi , Tsamadou Sofia , Anagnostopoulou Maria , Kofidou Danai , Gavriilidis Maxim , Mademtzoglou Despoina , Mavragani-Tsipidou Penelope
Published: August 2018

Chios mastic products are well-known for their broad applications in food industry, cosmetics, and healthcare since the antiquity. Given our recent finding that Chios mastic water (CMW) exerts antigenotoxic action, in the present study, we evaluated the genotoxic as well as the antigenotoxic potential of the four major compounds of CMW, namely, verbenone, α-terpineol, linalool, and trans-pinocarveol. The cytokinesis block micronucleus (CBMN) assay in cultured human lymphocytes and the Drosophila Somatic Mutation And Recombination Test (SMART), also known as the wing spot test, were employed. None of the four major CMW’s constituents or their mixtures showed genotoxic or recombinogenic activity in either of the assays used. Co-treatment of each of the constituents with MMC revealed that all except trans-pinocarveol exerted antigenotoxic potential. Moreover, co-administration of verbenone with linalool or α-terpineol presented statistically significant reduction of MMC-induced mutagenicity. In conclusion, the major CMW constituents were shown to be free of genotoxic effects, while some exerted antigenotoxic activity either alone or in combinations, suggesting synergistic phenomena. Our results provide evidence on the key antigenotoxicity effectors of the plant extract CMW.
Author Correction: The Significance of Interstitial Fibrosis on Left Ventricular Function in Hypertensive versus Hypertrophic Cardiomyopathy
Authors: Jiang Meng , Wang Zi , Su Xuan , Gong Xingrong , Pu Jun , Wu Lianming , Liu Chang , Yao Qiuying , Kong Lingcong , Xu Jianrong , Ben He
Published: August 2018

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.
Expression analysis and functional characterization of the mouse cysteine-rich with EGF-like domains 2
Authors: Oh-hashi Kentaro , Fujimura Keito , Norisada Junpei , Hirata Yoko
Published: August 2018

We have previously identified a novel endoplasmic reticulum (ER) stress-inducible protein, namely, cysteine-rich with EGF-like domains 2 (CRELD2), which is predominantly regulated by ATF6. However, few studies on intrinsic CRELD2 have been published. In the present study, we elucidated the expression of intrinsic CRELD2 in mouse tissues and ER stress- treated Neuro2a cells. Among nine tissues we tested, CRELD2 protein in the heart and skeletal muscles was negligible. CRELD2 expression in Neuro2a cells was induced at the late phase after treatment with tunicamycin (Tm) compared with rapid induction of growth arrest and DNA damage inducible gene 153 (GADD153). On the other hand, another ER stress inducer, thapsigargin, increased the intrinsic CRELD2 secretion from Neuro2a cells. We furthermore established CRELD2-deficient Neuro2a cells to evaluate their features. In combination with the NanoLuc complementary reporter system, which was designed to detect protein-protein interaction in living cells, CRELD2 interacted with not only CRELD2 itself but also with ER localizing proteins in Neuro2a cells. Finally, we investigated the responsiveness of CRELD2-deficient cells against Tm-treatment and found that CRELD2 deficiency did not affect the expression of genes triggered by three canonical ER stress sensors but rendered Neuro2a cells vulnerable to Tm-stimulation. Taken together, these findings provide the novel molecular features of CRELD2, and its further characterization would give new insights into understanding the ER homeostasis and ER stress-induced cellular dysfunctions.
Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster
Authors: Guio Lain , Vieira Cristina , González Josefa
Published: August 2018

Transposable elements are emerging as an important source of cis-acting regulatory sequences and epigenetic marks that could influence gene expression. However, few studies have dissected the role of specific transposable element insertions on epigenetic gene regulation. Bari-Jheh is a natural transposon that mediates resistance to oxidative stress by adding cis-regulatory sequences that affect expression of nearby genes. In this work, we integrated publicly available ChIP-seq and piRNA data with chromatin immunoprecipitation experiments to get a more comprehensive picture of Bari-Jheh molecular effects. We showed that Bari-Jheh was enriched for H3K9me3 in nonstress conditions, and for H3K9me3, H3K4me3 and H3K27me3 in oxidative stress conditions, which is consistent with expression changes in adjacent genes. We further showed that under oxidative stress conditions, H3K4me3 and H3K9me3 spread to the promoter region of Jheh1 gene. Finally, another insertion of the Bari1 family was associated with increased H3K27me3 in oxidative stress conditions suggesting that Bari1 histone marks are copy-specific. We concluded that besides adding cis-regulatory sequences, Bari-Jheh influences gene expression by affecting the local chromatin state.
Synergistic negative effects of thermal stress and altered food resources on echinoid larvae
Authors: Feehan Colette J. , Ludwig Zoe , Yu Suzannah , Adams Diane K.
Published: August 2018

Multiple changes to the marine environment under climate change can have additive or interactive (antagonistic or synergistic) effects on marine organisms. Prompted by observations of anomalously warm sea temperatures and low chlorophyll concentrations during the 2013–2016 warm “Blob” event in the Northeast Pacific Ocean, we examined the combined effects of thermal stress and a shift in food resources on the development of a larval echinoid (Strongylocentrotus droebachiensis) in the laboratory. A high concentration of phytoplankton yielded faster echinus rudiment development at warm versus historical temperature, indicating a mitigating effect of abundant food on thermal stress; however, low phytoplankton concentration or a shift in diet to suspended kelp detritus, yielded slow development and high mortality at warm temperature. The results indicate a synergistic negative effect of thermal stress and altered food resources on larvae of a keystone marine species.
Light-programmable manipulation of DC field in Laplacian Meta-devices
Authors: Han Tiancheng , Liu Yuexia , Liu Lei , Qin Jin , Li Ying , Bao Jiayu , Ni Dongyuan , Qiu Cheng-Wei
Published: August 2018

Impressive progresses have been achieved in the field of metamaterial to mimic the illusion or camouflage effects in nature. These include invisible cloaks and many other cloak-based illusion meta-devices. However, to date many experiments only present single, static or discretized functionalities. The dynamical control of multiple kinds of illusion signals can only be achieved by embedding complex active sources directly connected to external stimuli, leading to limited on/off switching effect in a contact fashion. Here, we experimentally demonstrate a distinct scheme to incorporate multi-functions into one passive Laplacian DC meta-device, assisted by light illumination. It is shown that light-programmable cloaking, full illusion, and partial illusion can be achieved on the same device without physical contact of the heating pads or electric bias, at the cost of only four kinds of natural bulk materials with homogeneous parameters throughout. A DC network is fabricated to demonstrate the proof of concept, with measurement results in good agreement with the numerical simulations. The proposed scheme may open a new avenue to the non-contact multiphysical control of multi-illusion functions for Laplacian fields.
Early molecular events associated with nitrogen deficiency in rice seedling roots
Authors: Hsieh Ping-Han , Kan Chia-Cheng , Wu Hsin-Yu , Yang Hsiu-Chun , Hsieh Ming-Hsiun
Published: August 2018

Nitrogen (N) deficiency is one of the most common problems in rice. The symptoms of N deficiency are well documented, but the underlying molecular mechanisms are largely unknown in rice. Here, we studied the early molecular events associated with N starvation (−N, 1 h), focusing on amino acid analysis and identification of −N-regulated genes in rice roots. Interestingly, levels of glutamine rapidly decreased within 15 min of −N treatment, indicating that part of the N-deficient signals could be mediated by glutamine. Transcriptome analysis revealed that genes involved in metabolism, plant hormone signal transduction (e.g. abscisic acid, auxin, and jasmonate), transporter activity, and oxidative stress responses were rapidly regulated by −N. Some of the −N-regulated genes encode transcription factors, protein kinases and protein phosphatases, which may be involved in the regulation of early −N responses in rice roots. Previously, we used similar approaches to identify glutamine-, glutamate-, and ammonium nitrate-responsive genes. Comparisons of the genes induced by different forms of N with the −N-regulated genes identified here have provided a catalog of potential N regulatory genes for further dissection of the N signaling pathwys in rice.
Curve-fitting techniques improve the mid-infrared analysis of soil organic carbon: a case study for Brookston clay loam particle-size fractions
Authors: Fan Ruqin , Yang Xueming , Drury Craig F. , Zhang Zhenhua
Published: August 2018

Few studies have evaluated structural features of soil organic carbon (SOC) in different soil particle fractions, especially SOC changes induced by tillage, using Fourier transformed mid-infrared (MIR) spectroscopy. To make a contribution in this context, soil samples of a Brookston clay loam (mesic Typic Argiaquoll) with averaged pH and organic matter concentration at 7.28 and 43.9 g kg−1, respectively, were collected from short-term no-tillage (NT97) and mouldboard plow (CT97) treatments initiated in 1997 and long-term no-tillage (NT83) and mouldboard plow (CT83) treatments initiated in 1983 under a corn-soybean rotation, and were separated into sand, silt, and clay fractions using sonication. Structural features of SOC in these soil fractions were investigated using curve-fitting analysis of mid-infrared (MIR) spectra. Aromatic C content was found to be greater in clay- than in sand-sized fractions, while aliphatic C content was higher in sand- than in silt- and clay-sized particles. With decrease in tillage intensity, the aliphatic C gradually increased in sand- and clay-sized fractions but not in the silt-sized fraction. The aliphatic C content in sand fraction was significantly greater in NT83 than CT83 (P < 0.05). The aromatic C in silt- and clay-sized fractions was greater in NT83 than in both CT soils, whereas aromatic C contents were higher in both CT soils than in NT83 soil. Significantly higher aromatic/aliphatic C ratio in CT83 than NT83 was found in sand-sized fractions, while the opposite trend was found in the silt-sized fraction. These findings were not apparent until the curve-fitting technique was employed, which has the capacity to quantify many overlapped bands in the spectra. This study demonstrates that the curve-fitting of MIR spectra advances the analysis of organic matter in soil samples.
Improvement of physico-chemical properties of dextran-chitosan composite scaffolds by addition of nano-hydroxyapatite
Authors: El-Meliegy Emad , Abu-Elsaad N. I. , El-Kady Abeer M. , Ibrahim Manar A.
Published: August 2018

Nano-hydroxyapatite was incorporated into polymer matrix of Dextran/Chitosan to achieve a novel composite scaffold by freeze drying technique. The synthesized composite scaffolds were recognized by different performances such as: X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR) and Scanning electron microscope (SEM). The results revealed the complex formation between dextran and chitosan with an excellent dispersion of nHA inside the polymer matrix. The SEM images showed the presence of interconnected pore structure inside the scaffolds. The porosity of the composites was found to decrease from 82% to 67% by adding nanohydroxyapatite to the polymer matrix of Dextran/Chitosan. The mechanical properties of the scaffolds were measured by compression test. The obtained results verified that the presence of nHA can noticeably enhance young’s modulus and compressive strength of the composite scaffolds. All the obtained results essentially recommend that these composites can be a good candidate for bone tissue engineering applications.
Fluorescence detection of DNA mismatch repair in human cells
Authors: Ito Shunsuke , Shiraishi Miyako , Tsuchihashi Kazuki , Takatsuka Reine , Yamamoto Junpei , Kuraoka Isao , Iwai Shigenori
Published: August 2018

Mismatched base pairs, produced by nucleotide misincorporation by DNA polymerase, are repaired by the mismatch repair (MMR) pathway to maintain genetic integrity. We have developed a method for the fluorescence detection of the cellular MMR ability. A mismatch, which would generate a stop codon in the mRNA transcript unless it was repaired, was introduced into the gene encoding the enhanced green fluorescent protein (EGFP) in an expression plasmid. When MMR-proficient HeLa cells were transformed with this plasmid, the production of active EGFP was observed by fluorescence microscopy. It was assumed that the nick required to initiate the MMR pathway was produced non-specifically in the cells. In contrast, fluorescence was not detected for three types of MMR-deficient cells, LoVo, HCT116, and DLD-1, transformed with the same plasmid. In addition, the expression of a red fluorescent protein gene was utilized to avoid false-negative results. This simple fluorescence method may improve the detection of repair defects, as a biomarker for cancer diagnosis and therapy.
Effect of medication adherence on long-term all-cause-mortality and hospitalization for cardiovascular disease in 65,067 newly diagnosed type 2 diabetes patients
Authors: Kim Yeon-Yong , Lee Jin-Seok , Kang Hee-Jin , Park Sang Min
Published: August 2018

This study determined the effects of anti-diabetic medication adherence on the long-term all-cause mortality and hospitalization for cerebrovascular disease and myocardial infarction among newly diagnosed patients. The study used retrospective cohort from the National Health Insurance Service. Study participants were 65,076 newly diagnosed type 2 diabetes mellitus patients aged ≥40 years. The medication adherence was evaluated from the proportion of days covered (PDC) between 2006 and 2007. Outcome variables were mortality, newly diagnosed cerebrovascular disease (CVD) and myocardial infarction (MI) in 2008–2017. Cox-proportional hazard regression analysis was performed. After adjusting for sex, age, monthly contribution, insurance type, medical institution type, Charlson comorbidity index score, disability, hypertension, and active ingredients of oral hypoglycemic agents, the adjusted hazard ratio (aHR) for all-cause-mortality of the lowest PDC group (<0.20) was 1.45 (95% confidence interval [CI] = 1.36–1.54) as compared to the highest PDC (≥0.8). The aHR for all-cause-mortality associated with PDC levels of 0.60–0.79, 0.40–0.59, and 0.20–0.39 were 1.19, 1.26, and 1.34, respectively (Ptrend < 0.001). Compared to the highest PDC group, diabetic patients with the lowest PDC had elevated risk for CVD (aHR = 1.41; 95% CI = 1.30–1.52;Ptrend < 0.001). Improving anti-diabetic medication adherence among newly diagnosed type 2 diabetes mellitus patients is essential to the reduce risk for cardiovascular disease and long-term all-cause mortality.
Author Correction: Stability of an adaptive hybrid community
Authors: Mougi Akihiko
Published: August 2018

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.
Wildfire-driven thunderstorms cause a volcano-like stratospheric injection of smoke
Authors: Peterson David A. , Campbell James R. , Hyer Edward J. , Fromm Michael D. , Kablick George P. , Cossuth Joshua H. , DeLand Matthew T.
Published: August 2018

Intense heating by wildfires can generate deep, smoke-infused thunderstorms, known as pyrocumulonimbus (pyroCb), which can release a large quantity of smoke particles above jet aircraft cruising altitudes. Injections of pyroCb smoke into the lower stratosphere have gained increasing attention over the past 15 years due to the rapid proliferation of satellite remote sensing tools. Impacts from volcanic eruptions and other troposphere-to-stratosphere exchange processes on stratospheric radiative and chemical equilibrium are well recognized and monitored. However, the role of pyroCb smoke in the climate system has yet to be acknowledged. Here, we show that the mass of smoke aerosol particles injected into the lower stratosphere from five near-simultaneous intense pyroCbs occurring in western North America on 12 August 2017 was comparable to that of a moderate volcanic eruption, and an order of magnitude larger than previous benchmarks for extreme pyroCb activity. The resulting stratospheric plume encircled the Northern Hemisphere over several months. By characterizing this event, we conclude that pyroCb activity, considered as either large singular events, or a full fire season inventory, significantly perturb the lower stratosphere in a manner comparable with infrequent volcanic intrusions.
Tropospheric OH and stratospheric OH and Cl concentrations determined from CH4, CH3Cl, and SF6 measurements
Authors: Li Mengze , Karu Einar , Brenninkmeijer Carl , Fischer Horst , Lelieveld Jos , Williams Jonathan
Published: August 2018

The hydroxyl (OH) radical is the key oxidant in the global atmosphere as it controls the concentrations of toxic gases like carbon monoxide and climate relevant gases like methane. In some regions, oxidation by chlorine (Cl) radical is also important, and in the stratosphere both OH and Cl radicals impact ozone. An empirical method is presented to determine effective OH concentrations in the troposphere and lower stratosphere, based on CH4, CH3Cl, and SF6 data from aircraft measurements (IAGOS-CARIBIC) and a ground-based station (NOAA). Tropospheric OH average values of 10.9 × 105 (σ = 9.6 × 105) molecules cm−3 and stratospheric OH average values of 1.1 × 105 (σ = 0.8 × 105) molecules cm−3 were derived over mean ages derived from SF6. Using CH4 led to higher OH estimates due to the temperature dependence of the CH4 + OH reaction in the troposphere and due to the presence of Cl in the stratosphere. Exploiting the difference in effective OH calculated from CH3Cl and CH4 we determine the main altitude for tropospheric CH4 oxidation to be 4.5 ~ 10.5 km and the average Cl radical concentration in the lower stratosphere to be 1.1 × 104 (σ = 0.6 × 104) molecules cm−3 (with a 35% measurement uncertainty). Furthermore, the data are used to examine the temporal trend in annual average stratospheric OH and Cl radical concentrations between 2010 and 2015. The year 2013 showed highest stratospheric OH and lowest Cl but no clear temporal trend was observed in the data in this period. These data serve as a baseline for future studies of stratospheric circulation changes.
Mesoporous SBA-15 modified with titanocene complexes and ionic liquids: interactions with DNA and other molecules of biological interest studied by solid state electrochemical techniques
Authors: del Hierro Isabel , Gómez-Ruiz Santiago , Pérez Yolanda , Cruz Paula , Prashar Sanjiv , Fajardo Mariano
Published: August 2018

The effect of the functionalization of SBA-15 with titanocene derivatives and ionic liquids in biological processes has been tested by electrochemical techniques.
Metal vapor synthesis of ultrasmall Pd nanoparticles functionalized with N-heterocyclic carbenes
Authors: Tegeder Patricia , Marelli Marcello , Freitag Matthias , Polito Laura , Lamping Sebastian , Psaro Rinaldo , Glorius Frank , Ravoo Bart Jan , Evangelisti Claudio
Published: August 2018

The synthesis of N-heterocyclic carbene (NHC)-stabilized palladium nanoparticles (PdNPs) by an entirely new strategy comprising the NHC functionalization of ligand-free PdNPs obtained by metal vapor synthesis is described.
Five monocyclic pyridinium derivative based halo-argentate/cuprate hybrids or iodide salts: influence of composition on photochromic behaviors
Authors: Yu Tan-Lai , Wu Guo-Xing , Xue Mei , Wang Zhong-Hui , Fu Yun-Long
Published: August 2018

Using novel monocyclic pyridinium derivatives as structural directing agents and electron acceptors, five composition dependent photochromic compounds have been synthesized.
The effect of the linker size in C2-symmetrical chiral ligands on the self-assembly formation of luminescent triple-stranded di-metallic Eu(iii) helicates in solution
Authors: Kotova Oxana , Comby Steve , Pandurangan Komala , Stomeo Floriana , O'Brien John E. , Feeney Martin , Peacock Robert D. , McCoy Colin P. , Gunnlaugsson Thorfinnur
Published: August 2018

The formation, stability constants and luminescence of chiral Eu(iii) supramolecular assemblies were studied in CH3CN.
Superhydrophilic phosphate and amide functionalized magnetic adsorbent: a new combination of anti-biofouling and uranium extraction from seawater
Authors: Guo Xuejie , Chen Rongrong , Liu Qi , Liu Jingyuan , Zhang Hongsen , Yu Jing , Li Rumin , Zhang Milin , Wang Jun
Published: August 2018

Phosphate and amide functionalized magnetic nanocomposites were successfully preparedvia in situsynthesis for the extraction of uranium from seawater combined with an antifouling property.
Multifunctional hydrogel enables extremely simplified electrochromic devices for smart windows and ionic writing boards
Authors: Fang Huajing , Zheng Pengyue , Ma Rong , Xu Chen , Yang Gaiying , Wang Qing , Wang Hong
Published: August 2018

A much simplified electrochromic structure for smart windows and ionic writing boards is designed based on a multifunctional hydrogel.
Iodine-mediated cross-dehydrogenative coupling of pyrazolones and alkenes
Authors: Yang Kai , Bao Xiaoze , Yao Ye , Qu Jingping , Wang Baomin
Published: August 2018

An iodine-mediated alkenylation of pyrazolones with simple alkenes under air has been developed, leading directly to alkenylated pyrazolone derivatives in good yield.
Artificial photosynthesis – from sunlight to fuels and valuable products for a sustainable future
Authors: Messinger Johannes , Ishitani Osamu , Wang Dunwei
Published: August 2018

This themed issue includes a collection of articles on artificial photosynthesis: from sunlight to fuels and valuable products for a sustainable future.
Material gradients in fibrillar insect attachment systems: the role of joint-like elements
Authors: Heepe Lars , Höft Sabrina , Michels Jan , Gorb Stanislav N.
Published: August 2018

A not yet described type of material gradient in discoidal setae of male leaf beetles is shown that is suggested to facilitate their adaptability to curved and non-parallel surfaces.
Correction: Nanofiltration membranes with cellulose nanocrystals as an interlayer for unprecedented performance
Authors: Wang Jing-Jing , Yang Hao-Cheng , Wu Ming-Bang , Zhang Xi , Xu Zhi-Kang
Published: August 2018

Correction for ‘Nanofiltration membranes with cellulose nanocrystals as an interlayer for unprecedented performance’ by Jing-Jing Wang et al., J. Mater. Chem. A, 2017, 5, 16289–16295.
Epitaxial ferroelectric Hf0.5Zr0.5O2 thin film on a buffered YSZ substrate through interface reaction
Authors: Li Tao , Zhang Nian , Sun Zhenzhong , Xie Chunxiao , Ye Mao , Mazumdar Sayantan , Shu Longlong , Wang Yu , Wang Danyang , Chen Lang , Ke Shanming , Huang Haitao
Published: August 2018

In this study, we used pulsed laser deposition to successfully grow epitaxial Hf0.5Zr0.5O2 (HZO) films on (001)-, (011)- and (111)-oriented yttria-stabilized zirconia (YSZ) substrates using TiN as the bottom electrode.
Multifunctional Pt(ii) metallomesogens exhibiting luminescence and proton conductivity in the mesophase near room temperature
Authors: Cuerva Cristián , Campo José A. , Cano Mercedes , Schmidt Rainer , Lodeiro Carlos
Published: August 2018

The first family of Pt(ii) metallomesogens with phosphorescence and dielectric properties that are operational near room temperature has been successfully obtained.
High-entropy alloy superconductors on an α-Mn lattice
Authors: Stolze Karoline , Cevallos F. Alex , Kong Tai , Cava Robert J.
Published: August 2018

Previously unreported High-Entropy Alloy (HEA) superconductors in the pentanary (ZrNb)1−x[MoReRu]x, (HfTaWIr)1−x[Re]x, and (HfTaWPt)1−x[Re]x systems are described and characterized.
Atomically thin semiconducting penta-PdP2 and PdAs2 with ultrahigh carrier mobility
Authors: Yuan Hao , Li Zhenyu , Yang Jinlong
Published: August 2018

Two dimensional materials with a pentagonal structure and ultra-high carrier mobilities have been designed theoretically.
Zero-thermal-quenching and photoluminescence tuning with the assistance of carriers from defect cluster traps
Authors: Chen Yali , Yu Binxun , Gou Jing , Liu Shengzhong Frank
Published: August 2018

The zero-thermal-quenching behavior at high temperature up to 225 °C was benefited from the carriers captured by deeper traps, which can be verified by thermoluminescence spectra.
Possibilities of using solar energy in the processes of cooling external zones of people
Authors: Dec Ewelina , Sekret Robert , Babiarz Bożena
Published: August 2018

Meteorological analyzes unambiguously indicate climate warming. An increase in average air temperatures is recorded in both winter and summer. In recent years, an increasing number of hot and very hot days are observed, and the duration of series of days with maximum daily temperature above 30°C is also longer. Occurrence of hot weather adversely affects the person staying outside. The ever-increasing requirements related to thermal comfort, enforce the provision of appropriate conditions not only in the rooms, but also in the external zones of people. Cooling the air in outdoor zones using standard air-conditioning systems can be expensive due to the high demand for electricity. Ensuring cooling through the use of renewable energy, such as solar energy, is a key solution to energy and environmental problems. In this article, the technical potential of solar radiation energy was determined based on data from the Rzeszow- Jasionka meteorological station and the possibilities of using solar energy in air cooling systems in external zones were presented.
Effect of Renal Impairment on the Pharmacokinetics and Pharmacodynamics of Tofogliflozin (A SELECTIVE SGLT2 Inhibitor) in Patients with Type 2 Diabetes Mellitus
Authors: Ikeda Sachiya , Takano Yasuki , Schwab Dietmar , Portron Agnes , Kasahara-Ito Nahoko , Saito Tomohisa , Iida Satofumi
Published: August 2018

Purpose Tofogliflozin is an orally available selective inhibitor of sodium-glucose co-transporter 2 for treatment of type 2 diabetes mellitus (T2DM). Two studies were conducted to evaluate the effect of renal impairment on pharmacokinetics and pharmacodynamics of tofogliflozin.

Methods The studies were: 1) single dose study in T2DM patients with normal renal function and mild, moderate and severe renal impairment, and 2) multiple dose study for 24 weeks in T2DM patients with normal renal function and moderate renal impairment.

Results Renal function did not have a clinically relevant effect on the PK of tofogliflozin. Urinary glucose excretion up to 24 h after administration of tofogliflozin (UGE24h) decreased with decreasing glomerular filtration rate. Lowering UGE24h resulted in waning glycemic control but not body weight reduction.

Conclusions Single and multiple administrations of tofogliflozin were generally well tolerated in T2DM patients with various renal functions. As far as investigated here, these studies indicate no dose adjustment is required for patients with renal impairment.
Facile Synthesis of Halogen Decorated para-/meta-Hydroxy­benzoates by Iridium-Catalyzed Borylation and Oxidation
Authors: Chotana Ghayoor , Shahzadi Tayyaba , Saleem Rahman
Published: August 2018

Hydroxybenzoates are an important class of phenols that are widely used as preservatives and antiseptics in the food and pharmaceutical industries. In this report, a facile preparation of 2,6- and 2,3-disubstituted 4/5-hydroxybenzoates by iridium-catalyzed borylation of respective disubstituted benzoate esters followed by oxidation is described. This synthetic route allows for the incorporation of halogens in the final hydroxybenzoates with substitution patterns not readily accessible by the traditional routes of aromatic functionalization.
Cardiopulmonary Function in Thoracic Wall Deformities: What Do We Really Know?
Authors: Velazco Cristine , Pulivarthi Venkata , Arsanjani Reza , Obermeyer Robert , Jaroszewski Dawn
Published: August 2018

Patients with pectus excavatum (PE) frequently present with complaints of exercise intolerance and cardiopulmonary symptoms. There continues to be controversy regarding the physiologic benefits of repair. The aim of this review is to summarize and discuss recent data regarding the cardiopulmonary effects of PE deformity and the evidence for improvement obtained after surgical repair including (1) a greater efficiency of breathing (chest wall mechanics), (2) improvement in pulmonary restrictive deficits, (3) an increase in cardiac chamber size and output, with improved cardiac strain and strain rate, and (4) improvement in exercise capacity.
Increasing power and torque capability of brushless direct current motor by employing 150-degree conduction mode controlled three-phase voltage source inverter
Authors: Ozgenel Mehmet Cihat
Published: August 2018

With the reduction of magnet costs and the production of high-energy magnets in small sizes, permanent magnet brushless motors are used widely in various applications from household to medical, industrial, and automation applications. Furthermore, permanent magnet brushless motors have some significant advantages over the other conventional motors such as induction and brushed motors. Due to the popularity of brushless motors, they have become the focus of interest of researchers. From the past 30 years to today, the researchers have carried out numerous studies in relation to brushless motors. These studies are generally sensorless control, adaptive control, different Proportional Integral and Derivate (PID) applications, fuzzy control, PI-fuzzy and PID-fuzzy control and different Pulse Width Modulation applications and to eliminate torque ripple and other control algorithms. Permanent magnet brushless motors can be divided into two main groups. One is the permanent magnet synchronous motor and the other one is the permanent magnet brushless direct current motor (BLDCM). BLDC motors are the most preferred in applications due to their low cost and relatively simple drivers. BLDC motors are run with the classical 120-degree conduction mode voltage source inverter (VSI). Because BLDC motors run with 120-degree conduction mode inverters, power and torque produced by BLDC motors are less than their capacity, whereas BLDC motors can provide a better dynamic response, higher power, and torque by employing 150-degree conduction mode controlled VSI. In this experimental study, it is aimed to design and manufacture a versatile VSI which can control the BLDC motor in both 120 and 150–degree conduction modes. Then, BLDC motor is run in two conduction modes employing the purposed inverter under various loads, and the torque, power, and speed performance of the motor were analyzed to demonstrate the effect of the two commutation methods on BLDC motor performance. The results of this comparative experimental study have shown that the 150-degree conduction mode-controlled inverter provides with the BLDC motor generating higher power, torque, and speed than the inverter with 120-degree conduction mode.
Electrical driving of X-band mechanical waves in a silicon photonic circuit
Authors: Van Laer Raphaël , Patel Rishi N. , McKenna Timothy P. , Witmer Jeremy D. , Safavi-Naeini Amir H.
Published: August 2018

Reducing energy dissipation is a central goal of classical and quantum technologies. Optics achieved great success in bringing down power consumption of long-distance communication links. With the rise of mobile, quantum, and cloud technologies, it is essential to extend this success to shorter links. Electro-optic modulators are a crucial contributor of dissipation in such links. Numerous variations on important mechanisms such as free-carrier modulation and the Pockels effect are currently pursued, but there are few investigations of mechanical motion as an electro-optic mechanism in silicon. In this work, we demonstrate electrical driving and optical read-out of a 7.2 GHz mechanical mode of a silicon photonic waveguide. The electrical driving is capacitive and can be implemented in any material system. The measurements show that the mechanically mediated optical phase modulation is two orders of magnitude more efficient than the background phase modulation in our system. Our demonstration is an important step toward efficient opto-electro-mechanical devices in a scalable photonic platform.
Effect of self-bias on cylindrical capacitive discharge for processing of inner walls of tubular structures—Case of SRF cavities
Authors: Upadhyay J. , Peshl J. , Popović S. , Valente-Feliciano A.-M. , Vušković L.
Published: August 2018

Cylindrical capacitive discharge is a convenient medium for generating reactive ions to process inner walls superconductive radio-frequency (SRF) cavities. These cavities, used in particle accelerators, presents a three-dimensional structure made of bulk Niobium, with axial cylindrical symmetry. Manufactured cavity walls are covered with Niobium oxides and scattered particulates, which must be removed for desired SRF performance. Cylindrical capacitive discharge in a mixture of Ar and Cl2 is a sole and natural non-wet acid choice to purify the inner surfaces of SRF cavities by reactive ion etching. Coaxial cylindrical discharge is generated between a powered inner electrode and the grounded outer electrode, which is the cavity wall to be etched. Plasma sheath voltages were tailored to process the outer wall by providing an additional dc current to the inner electrode with the help of an external compensating dc power supply and corrugated design of the inner electrode. The dc bias potential difference is established between two electrodes to make the set-up favorable for SRF wall processing. To establish guidelines for reversing the asymmetry and establishing the optimal sheath voltage at the cavity wall, the dc self-bias potential and dc current dependence on process parameters, such as gas pressure, rf power and chlorine content in the Ar/Cl2 gas mixture was measured. The process is potentially applicable to all concave metallic surfaces.
Finding recurrence in chaos: New quantifier helps predict repeating events
Authors: Liebendorfer Adam
Published: August 2018

A nonlinear quantifier, developed by defining submatrix microstates within recurrence matrices, has broad-reaching implications ranging from economics to physics and beyond.
Optical fiber approach diagnoses fast electrons in laser experiments
Authors: Liebendorfer Adam
Published: August 2018

A technique for measuring fast electrons provides new avenues to understanding absorption processes in repeating ultra-intense laser pulse experiments.
Navigating the fiery debate: the role of scientific evidence in eliciting policy and management responses for contentious plants in northern Australia
Authors: Setterfield Samantha A. , Rossiter-Rachor Natalie A. , Adams Vanessa M.
Published: August 2018

Australia’s vast tropical savannas contain outstanding biodiversity and cultural values. The region supports many industries, with broad-scale pastoralism being the most widespread. Hundreds of plant species were introduced into northern Australia to support the pastoral industry; some species have since been termed ‘contentious’ or ‘conflict’ species due to their perceived positive value for industry but negative impacts on non-pastoral values when they invaded non-pastoral landscapes. Heated political and public debate ensued about the appropriate policy and management response to these species based on people’s perceptions of values being altered by invasion by these species, and conflicting views on what constituted appropriate management actions to control their use and spread. Here we share our insights into the role of scientific evidence in progressing this debate, by quantifying the impacts of species on environmental, socioeconomic and cultural values. We reflect on the importance of science for underpinning evidence-based risk management tools, the outputs of which supported policy response by politicians and other policy decision-makers. We also assess the gap in translation from policy to coordinated on-ground action at the national scale, and provide our insights into the contribution that science can make to bridging this gap.
How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?
Authors: Jing Xiaobo , Loskot Pavel , Yu Jin
Published: August 2018

Transcription plays an essential role in gene expression. The transcription bursting in bacteria has been suggested to be regulated by positive supercoiling accumulation in front of a transcribing RNA polymerase (RNAP) together with gyrase binding on DNA to release the supercoiling. In this work, we study the supercoiling regulation in the case of a battery of RNAPs working together on DNA by constructing a multi-state quantitative model, which allows gradual and stepwise supercoiling accumulation and release in the RNAP transcription. We solved for transcription characteristics under the multi-state bursting model for a single RNAP transcription, and then simulated for a battery of RNAPs on DNA with T7 and Escherichia coli RNAP types of traffic, respectively, probing both the average and fluctuation impacts of the supercoiling regulation. Our studies show that due to the supercoiling accumulation and release, the number of RNAP molecules loaded onto the DNA vary significantly along time in the traffic condition. Though multiple RNAPs in transcription promote the mRNA production, they also enhance the supercoiling accumulation to suppress the production. In particular, the fluctuations of the mRNA transcripts become highly pronounced for a battery of RNAPs transcribing together under the supercoiling regulation, especially for a long process of transcription elongation. In such an elongation process, though a single RNAP can work at a high duty ratio, multiple RNAPs are hardly able to do so. Our multi-state model thus provides a systematical characterization of the quantitative features of the bacterial transcription bursting; it also supports improved physical examinations on top of this general modeling framework.
CharGer: clinical Characterization of Germline variants
Authors: Scott Adam D , Huang Kuan-Lin , Weerasinghe Amila , Mashl R Jay , Gao Qingsong , Martins Rodrigues Fernanda , Wyczalkowski Matthew A , Ding Li
Published: August 2018

CharGer (Characterization of Germline variants) is a software tool for interpreting and predicting clinical pathogenicity of germline variants. CharGer gathers evidence from databases and annotations, provided by local tools and files or via ReST APIs, and classifies variants according to ACMG guidelines for assessing variant pathogenicity. User-designed pathogenicity criteria can be incorporated into CharGer’s flexible framework, thereby allowing users to create a customized classification protocol.

Availability and implementation

Source code is freely available at https://github.com/ding-lab/CharGer and is distributed under the GNU GPL-v3.0 license. Software is also distributed through the Python Package Index (PyPI) repository. CharGer is implemented in Python 2.7 and is supported on Unix-based operating systems.

Supplementary information

Supplementary data are available at Bioinformatics online.
Impacts of small-scale fisheries on mangrove fish assemblages
Authors: Reis-Filho José Amorim , Harvey Euan S , Giarrizzo Tommaso
Published: August 2018

The data requirements and resources needed to develop effective indicators of fishing impacts on target stocks may often be great, especially for mangrove fisheries where, for example, tidal cycles sequentially flood and drain the habitat as a result of natural processes. Here, we used underwater video systems to evaluate the impact of small-scale fisheries on mangrove fish assemblages at four levels of fishing pressure (low, medium, high, and no pressure). The lowest values of species richness and abundance were recorded in the areas fished most intensively. Conversely, the highest species richness and the occurrence of larger-bodied fish were recorded in areas of reduced fishing activity, which was surprisingly similar to the “no fishing” areas. The slopes of the community size spectra steepened in response to exploitation, while the relative abundance of medium-sized fish (16–25 cm) declined. Fishing for local or regional markets, rather than subsistence, also led to a decrease in the abundance of larger fish (>41 cm). The marked response of population parameters to fishing pressure reflected the impact of unregulated small-scale fisheries on areas of mangroves. Fishery management practices that ignore contemporary changes in these environments are likely to overestimate long-term yields, leading to overfishing. Thus, size-based approaches to evaluating fishing pressure were suitable for detecting negative responses from the mangrove fish assemblages. A next step will be to integrate size- and species-based ecological approaches that provide mechanisms to address pronounced decreases in specific species as a more profitable indicator of fishing impacts on mangrove fish assemblages. This approach will allow the development of effective conservation and management strategies.