bluuebunny/crossref_metadata_2025 huggingface dataset:
A new method for measuring lung deposition efficiency of airborne nanoparticles in a single breath
Authors: Jakobsson Jonas K. F. , Hedlund Johan , Kumlin John , Wollmer Per , Löndahl Jakob
Published: November 2016

Assessment of respiratory tract deposition of nanoparticles is a key link to understanding their health impacts. An instrument was developed to measure respiratory tract deposition of nanoparticles in a single breath. Monodisperse nanoparticles are generated, inhaled and sampled from a determined volumetric lung depth after a controlled residence time in the lung. The instrument was characterized for sensitivity to inter-subject variability, particle size (22, 50, 75 and 100 nm) and breath-holding time (3–20 s) in a group of seven healthy subjects. The measured particle recovery had an inter-subject variability 26–50 times larger than the measurement uncertainty and the results for various particle sizes and breath-holding times were in accordance with the theory for Brownian diffusion and values calculated from the Multiple-Path Particle Dosimetry model. The recovery was found to be determined by residence time and particle size, while respiratory flow-rate had minor importance in the studied range 1–10 L/s. The instrument will be used to investigate deposition of nanoparticles in patients with respiratory disease. The fast and precise measurement allows for both diagnostic applications, where the disease may be identified based on particle recovery, and for studies with controlled delivery of aerosol-based nanomedicine to specific regions of the lungs.
Differential selective pressure alters rate of drug resistance acquisition in heterogeneous tumor populations
Authors: Sun Daphne , Dalin Simona , Hemann Michael T. , Lauffenburger Douglas A. , Zhao Boyang
Published: November 2016

Recent drug discovery and development efforts have created a large arsenal of targeted and chemotherapeutic drugs for precision medicine. However, drug resistance remains a major challenge as minor pre-existing resistant subpopulations are often found to be enriched at relapse. Current drug design has been heavily focused on initial efficacy, and we do not fully understand the effects of drug selective pressure on long-term drug resistance potential. Using a minimal two-population model, taking into account subpopulation proportions and growth/kill rates, we modeled long-term drug treatment and performed parameter sweeps to analyze the effects of each parameter on therapeutic efficacy. We found that drugs with the same overall initial kill may exert differential selective pressures, affecting long-term therapeutic outcome. We validated our conclusions experimentally using a preclinical model of Burkitt’s lymphoma. Furthermore, we highlighted an intrinsic tradeoff between drug-imposed overall selective pressure and rate of adaptation. A principled approach in understanding the effects of distinct drug selective pressures on short-term and long-term tumor response enables better design of therapeutics that ultimately minimize relapse.
The transgenerational inheritance of autism-like phenotypes in mice exposed to valproic acid during pregnancy
Authors: Choi Chang Soon , Gonzales Edson Luck , Kim Ki Chan , Yang Sung Min , Kim Ji-Woon , Mabunga Darine Froy , Cheong Jae Hoon , Han Seol-Heui , Bahn Geon Ho , Shin Chan Young
Published: November 2016

Autism spectrum disorder (ASD) is a heterogeneously pervasive developmental disorder in which various genetic and environmental factors are believed to underlie its development. Recently, epigenetics has been suggested as a novel concept for ASD aetiology with a proposition that epigenetic marks can be transgenerationally inherited. Based on this assumption of epigenetics, we investigated the transgenerational inheritance of ASD-like behaviours and their related synaptic changes in the VPA animal model of ASD. The first generation (F1) VPA-exposed offspring exhibited autistic-like impaired sociability and increased marble burying. They also showed increased seizure susceptibility, hyperactivity and decreased anxiety. We mated the VPA-exposed F1 male offspring with naïve females to produce the second generation (F2), and then similarly mated the F2 to deliver the third generation (F3). Remarkably, the autism-like behavioural phenotypes found in F1 persisted to the F2 and F3. Additionally, the frontal cortices of F1 and F3 showed some imbalanced expressions of excitatory/inhibitory synaptic markers, suggesting a transgenerational epigenetic inheritance. These results open the idea that E/I imbalance and ASD-like behavioural changes induced by environmental insults in mice can be epigenetically transmitted, at least, to the third generation. This study could help explain the unprecedented increase in ASD prevalence.
The PTEN phosphatase functions cooperatively with the Fanconi anemia proteins in DNA crosslink repair
Authors: Vuono Elizabeth A. , Mukherjee Ananda , Vierra David A. , Adroved Morganne M. , Hodson Charlotte , Deans Andrew J. , Howlett Niall G.
Published: November 2016

Fanconi anemia (FA) is a genetic disease characterized by bone marrow failure and increased cancer risk. The FA proteins function primarily in DNA interstrand crosslink (ICL) repair. Here, we have examined the role of the PTEN phosphatase in this process. We have established that PTEN-deficient cells, like FA cells, exhibit increased cytotoxicity, chromosome structural aberrations, and error-prone mutagenic DNA repair following exposure to ICL-inducing agents. The increased ICL sensitivity of PTEN-deficient cells is caused, in part, by elevated PLK1 kinase-mediated phosphorylation of FANCM, constitutive FANCM polyubiquitination and degradation, and the consequent inefficient assembly of the FA core complex, FANCD2, and FANCI into DNA repair foci. We also establish that PTEN function in ICL repair is dependent on its protein phosphatase activity and ability to be SUMOylated, yet is independent of its lipid phosphatase activity. Finally, via epistasis analysis, we demonstrate that PTEN and FANCD2 function cooperatively in ICL repair.
A Novel Non-Peptidic Agonist of the Ghrelin Receptor with Orexigenic Activity In vivo
Authors: Pastor-Cavada Elena , Pardo Leticia M. , Kandil Dalia , Torres-Fuentes Cristina , Clarke Sarah L. , Shaban Hamdy , McGlacken Gerard P. , Schellekens Harriet
Published: November 2016

Loss of appetite in the medically ill and ageing populations is a major health problem and a significant symptom in cachexia syndromes, which is the loss of muscle and fat mass. Ghrelin is a gut-derived hormone which can stimulate appetite. Herein we describe a novel, simple, non-peptidic, 2-pyridone which acts as a selective agonist for the ghrelin receptor (GHS-R1a). The small 2-pyridone demonstrated clear agonistic activity in both transfected human cells and mouse hypothalamic cells with endogenous GHS-R1a receptor expression. In vivo tests with the hit compound showed significant increased food intake following peripheral administration, which highlights the potent orexigenic effect of this novel GHS-R1a receptor ligand.
Global Changes in Lipid Profiles of Mouse Cortex, Hippocampus, and Hypothalamus Upon p53 Knockout
Authors: Lee Sang Tak , Lee Jong Cheol , Kim Jong Whi , Cho Soo Young , Seong Je Kyung , Moon Myeong Hee
Published: November 2016

Comprehensive lipidomic profiling in three different brain tissues (cortex, hippocampus, and hypothalamus) of mouse with p53 deficiency was performed by nanoflow liquid chromatography-tandem mass spectrometry (nLC-MS/MS) and the profile was compared with that of the wild type. p53 gene is a well-known tumour suppressor that prevents genome mutations that can cause cancers. More than 300 lipids (among 455 identified species), including phospholipids (PLs), sphingolipids, ceramides (Cers), and triacylglycerols (TAGs) were quantitatively analysed by selective reaction monitoring (SRM) of nanoflow ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry (nUPLC-ESI-MS/MS). Among the three different neural tissues, hypothalamus demonstrated the most evident lipid profile changes upon p53 knockout. Alterations of PLs containing acyl chains of docosahexaenoic acid and arachidonic acid (highly enriched polyunsaturated fatty acids in the nervous system) were examined in relation to cell apoptosis upon p53 knockout. Comparison between sphingomyelins (SMs) and Cers showed that the conversion of SM to Cer did not effectively progress in the hypothalamus, resulting in the accumulation of SMs, possibly due to the inhibition of apoptosis caused by the lack of p53. Furthermore, TAGs were considerably decreased only in the hypothalamus, indicative of lipolysis that led to substantial weight loss of adipose tissue and muscles.
In ovo uptake, metabolism, and tissue-specific distribution of chiral PCBs and PBDEs in developing chicken embryos
Authors: Li Zong-Rui , Luo Xiao-Jun , Huang Li-Qian , Mai Bi-Xian
Published: November 2016

Fertilized chicken eggs were injected with environmental doses of 4 chiral polychlorinated biphenyls (PCBs) and 8 polybrominated biphenyl ethers (PBDEs) to investigate their uptake, metabolism in the embryo, and distribution in the neonate chicken. PCB95 uptake was the most efficient (80%) whereas BDE209 was the least (56%). Embryos metabolized approximately 52% of the PCBs absorbed. Though some degree of metabolism in the first 18 days, most of the PCBs and PBDEs was metabolized in the last three days, when BDE85, 99, 153, and 209 decrease by 11–37%. Enantioselective metabolism of the (+) enantiomers of PCB95, 149, and 132 and the (−) enantiomer of PCB91 was observed. The enantioselective reactivity was higher with the two penta-PCBs than the two tetra-PCBs. Liver, exhibited high affinity for high lipophilic chemicals, enrich all chemicals that was deflected in other tissues except for some special chemicals in a given tissues. Lipid composition, time of organ formation, and metabolism contribute to the distribution of chemicals in the neonate chicken. The result of this study will improve our understanding on the fate and potential adverse effects of PCBs and PBDEs in the neonate chicken.
An active IGF-1R-AKT signaling imparts functional heterogeneity in ovarian CSC population
Authors: Singh Ram K. , Dhadve Ajit , Sakpal Asmita , De Abhijit , Ray Pritha
Published: November 2016

Deregulated IGF-1R-AKT signaling influences multiple nodes of cancer cell physiology and assists in migration, metastasis and acquirement of radio/chemoresistance. Enrichment of cancer stem cells (CSC) positively correlates with radio/chemoresistance development in various malignancies. It is unclear though, how IGF-1R-AKT signalling shapes CSC functionality especially in ovarian cancer. Previously we showed that upregulated IGF-1R expression is essential to initiate platinum-taxol resistance at early stage which declines with elevated levels of activated AKT at late resistant stage in ovarian cancer cells. Here, we investigated the effect of this oscillatory IGF-1R-AKT signalling upon CSC functionality during generation of chemoresistance. While gradual increase in CSC properties from early (ER) to late (LR) resistant stages was observed in three different (cisplatin/paclitaxel/cisplatin-paclitaxel) cellular models created in two ovarian cancer cell lines, the stemness gene expressions (oct4/sox2/nanog) reached a plateau at early resistant stages. Inhibition of IGF-1R only at ER and AKT inhibition only at LR stages significantly abrogated the CSC phenotype. Interestingly, real time bioluminescence imaging showed CSCs of ER stages possessed faster tumorigenic potential than CSCs belonging to LR stages. Together, our data suggest that IGF-1R-AKT signalling imparts functional heterogeneity in CSCs during acquirement of chemoresistance in ovarian carcinoma.
Sequencing of long stretches of repetitive DNA
Authors: De Bustos Alfredo , Cuadrado Angeles , Jouve Nicolás
Published: November 2016

Repetitive DNA is widespread in eukaryotic genomes, in some cases making up more than 80% of the total. SSRs are a type of repetitive DNA formed by short motifs repeated in tandem arrays. In some species, SSRs may be organized into long stretches, usually associated with the constitutive heterochromatin. Variation in repeats can alter the expression of genes, and changes in the number of repeats have been linked to certain human diseases. Unfortunately, the molecular characterization of these repeats has been hampered by technical limitations related to cloning and sequencing. Indeed, most sequenced genomes contain gaps owing to repetitive DNA-related assembly difficulties. This paper reports an alternative method for sequencing of long stretches of repetitive DNA based on the combined use of 1) a linear vector to stabilize the cloning process, and 2) the use of exonuclease III for obtaining progressive deletions of SSR-rich fragments. This strategy allowed the sequencing of a fragment containing a stretch of 6.2 kb of continuous SSRs. To demonstrate that this procedure can sequence other kinds of repetitive DNA, it was used to examine a 4.5 kb fragment containing a cluster of 15 repeats of the 5S rRNA gene of barley.
Comparative morphological trade-offs between pre- and post-copulatory sexual selection in Giant hissing cockroaches (Tribe: Gromphadorhini)
Authors: Durrant Kate L. , Skicko Ian M. , Sturrock Craig , Mowles Sophie L.
Published: November 2016

Sperm competition theory predicts that animals face a trade-off between investment in weaponry and investment in ejaculate composition. Within the Madagascan giant hissing cockroaches (Tribe Gromphadorhini) differences in morphology exist that may indicate differing strategies of male-male competition. We compared relative pronotal horn length using high-resolution X-ray CT scanning data, relative testes mass, and male-male agonistic behaviour between two species of hissing cockroaches, Gromphadorhina oblongonota and Aeluropoda insignis. The gross morphology and behaviour of these two species indicated that G. oblongonota is selected for pre-copulatory mate acquisition and that A. insignis is selected for post-copulatory sperm competition. We found evidence for a trade-off when investing in testes mass vs. horn length between the species. The large, aggressive G. oblongonota follows a strategy of greater investment in weapons at the expense of testes mass while the smaller, less-aggressive A. insignis invests in relatively greater testes mass and less in pronotal weapon length. We also found evidence of a trade-off within each species, where individuals invest more heavily in weapon length at the expense of testes mass. These findings support the predictions of pre- and post-copulatory competitive investment trade-offs for a relatively understudied Tribe of cockroaches.
One step microwave-assisted synthesis of nanocrystalline WOx–ZrO2 acid catalysts
Authors: Gonell Francisco , Portehault David , Julián-López Beatriz , Vallé Karine , Sanchez Clément , Corma Avelino
Published: November 2016

One-step microwave synthesis allows one to tune WOx species and ZrO2 polymorphs showing different activities in acid reactions.
Enhanced hydrogen storage properties of MgH2 co-catalyzed with K2NiF6 and CNTs
Authors: Sulaiman N. N. , Ismail M.
Published: November 2016

The active species KF, KH and Mg2Ni together with the unique structure of the CNTs functioned as a real catalyst.
Growth, physicochemical and quantum chemical investigations on 2-amino 5-chloropyridinium 4-carboxybutanoate – an organic crystal for biological and optoelectronic device applications
Authors: Babu B. , Chandrasekaran J. , Mohanbabu B. , Matsushita Yoshitaka , Saravanakumar M.
Published: November 2016

Optically transparent organic single crystals of 2-amino 5-chloropyridinium 4-carboxybutanoate (2A5C4C) with sizes of 7 × 4 × 2 mm3 were grown by a slow evaporation solution growth technique at room temperature using methanol solvent.
FESEM and XPS studies of ZrO2modified electrodeposited NiCoCrAlY nanocomposite coating subjected to hot corrosion environment
Authors: Srivastava Meenu , Bera Parthasarathi , Balaraju J. N. , Ravisankar B.
Published: November 2016

The aim of this study is to investigate the influence of Co and ZrO2, addition on the hot corrosion behavior of NiCrAlY electrodeposited nanocomposite coatings.
Electrical impedance monitoring of protein unfolding
Authors: de Lima Sandro V. , de Oliveira Helinando P. , de Melo Celso P.
Published: November 2016

We have applied electrical impedance spectroscopy (EIS) to investigate how the dielectric characteristics of protein aqueous solutions respond to varying amounts of a co-dissolved surfactant.
Active hydrogenation Rh nanocatalysts protected by new self-assembled supramolecular complexes of cyclodextrins and surfactants in water
Authors: Thanh Chau Nguyet Trang , Menuel Stéphane , Colombel-Rouen Sophie , Guerrero Miguel , Monflier Eric , Philippot Karine , Denicourt-Nowicki Audrey , Roucoux Alain
Published: November 2016

New supramolecular assemblies as protective agents of rhodium(0) nanoparticles for hydrogenation of various substrates in water.
Large areal mass, flexible and freestanding polyaniline/bacterial cellulose/graphene film for high-performance supercapacitors
Authors: Liu Rong , Ma Lina , Huang Shu , Mei Jia , Xu Jun , Yuan Guohui
Published: November 2016

Flexible and freestanding electrodes with high mass loading in the range of 7–13 mg cm−2 made of polyaniline (PANI)/bacterial cellulose (BC)/graphene (GN) conductive paper through a simple filtering method.
Binaphthyl-incorporated π-conjugated polymer/gold nanoparticle hybrids: a facile size- and shape-tailored synthesis
Authors: Song Sun Gu , Ha Seonggyun , Seo Kyeong-Bae , Lee Jookyeong , Choi Tae-Lim , Premkumar Thathan , Song Changsik
Published: November 2016

Size and shape of in situ synthesized polymer/gold nanocomposites were controlled by the solvents utilized and the molecular weights of the binaphthyl-incorporated π-conjugated polymers.
Synthesis of TiO2@C nanospheres with excellent electrochemical properties
Authors: Ding Jing , Gao Xian , Cha Limei , Cai Mei-Qiu , Ma Jianmin
Published: November 2016

TiO2@C nanospheres could exhibit a discharge capacity of 286.5 mA h g−1 at 100 mA g−1 after 200 cycles.
An oxygen tolerance conductive hydrogel anode membrane for use in a potentially implantable glucose fuel cell
Authors: Liu Shumin , Zheng Yudong , Sun Yi , Su Lei , Yue Lina , Wang YanSen , Feng Jingxuan , Fan Jinsheng
Published: November 2016

Schematic of the PtNPs/MWCNTs/BC anode membrane.
Effects of NaCl concentration on wear–corrosion behavior of SAF 2507 super duplex stainless steel
Authors: Han Gaofeng , Jiang Pengfei , Wang Jianzhang , Yan Fengyuan
Published: November 2016

Wear–corrosion behavior of SAF 2507 super duplex stainless steel (SDSS) in different concentrations of NaCl (from 0.5% to 8%, w/v) was investigated using a pin-on-disk tester.
Evaluation of different metal salt solutions for the preparation of solar cells with wide-gap Cu2ZnGeSxSe4−x absorbers
Authors: Schnabel T. , Seboui M. , Ahlswede E.
Published: November 2016

In this work, thin-film solar cells with a kesterite-type Cu2ZnGeSxSe4−x (CZGSSe) absorber were prepared from four different metal salt solutions.
Enhanced photocatalytic activity on polarized ferroelectric KNbO3
Authors: Fu Qiang , Wang Xianjie , Li Changyu , Sui Yu , Han Yaping , Lv Zhe , Song Bo , Xu Ping
Published: November 2016

In this paper, we demonstrate the enhanced photodegradation of rhodamine B on polarized ferroelectric KNbO3 (KNO) particles.
Diastereoselective synthesis of cyclopentene spiro-rhodanines containing three contiguous stereocenters via phosphine-catalyzed [3 + 2] cycloaddition or one-pot sequential [3 + 2]/[3 + 2] cycloaddition
Authors: Zhang Jiayong , Zhang Minxuan , Li Yuming , Liu Shang , Miao Zhiwei
Published: November 2016

5-Spiro-cyclopentene-rhodanine derivatives have been synthesized through two different diastereoselective phosphine-catalyzed cascade reactions in excellent diastereoselectivities and good to excellent yields.
The exclusive response of LSPR in uncapped gold nanoparticles towards silver ions and gold chloride ions
Authors: Tyagi Himanshu , Khan Tuhin , Mohapatra Jeotikanta , Mitra Arijit , Kalita Hemen , Aslam Mohammed
Published: November 2016

LSPR of gold nanoparticles supported over glass or silica nanoparticles modulated using simple ionic treatment.
Hyalodendriellins A–F, new 14-membered resorcylic acid lactones from the endophytic fungus Hyalodendriella sp. Ponipodef12
Authors: Lai Daowan , Mao Ziling , Xu Dan , Zhang Xuping , Wang Ali , Xie Rushan , Zhou Ligang , Liu Yang
Published: November 2016

Six new 14-membered resorcylic acid lactones (RALs), named hyalodendriellins A–F (1–6), were isolated from the culture of the endophytic fungus Hyalodendriella sp.
Broadband light absorption by silver nanoparticle decorated silica nanospheres
Authors: Rahman Md. Mahfuzur , Younes Hammad , Lu Jin You , Ni George , Yuan Shaojun , Fang Nicholas X. , Zhang TieJun , Al Ghaferi Amal
Published: November 2016

Ag NPs decorated SiO2 nanospheres for plasmon enhanced light absorption.
Asymmetric supercapacitors based on a NiCo2O4/three dimensional graphene composite and three dimensional graphene with high energy density
Authors: Sun Shumin , Wang Shen , Li Shaodan , Li Yannan , Zhang Yonghui , Chen Junli , Zhang Zhihong , Fang Shaoming , Wang Peiyuan
Published: November 2016

Asymmetric supercapacitors based on a NiCo2O4/3D-G composite and 3D-G show excellent supercapacitive performance with high energy density and long cycle life.
Biomass-derived interconnected carbon nanoring electrochemical capacitors with high performance in both strongly acidic and alkaline electrolytes
Authors: Wei Xianjun , Li Yongbin , Gao Shuyan
Published: November 2016

The match between sustainable electrode materials and electrolytes is the key to achieve high-rate electrochemical capacitors.
Vertically aligned ZnO–Au@CdS core–shell nanorod arrays as an all-solid-state vectorial Z-scheme system for photocatalytic application
Authors: Zhang Nan , Xie Shunji , Weng Bo , Xu Yi-Jun
Published: November 2016

Vertically aligned ZnO–Au@CdS core–shell nanorod arrays have been constructed and used as an all-solid-state vectorial Z-scheme system for photocatalytic application.
WO3 nanosponge photoanodes with high applied bias photon-to-current efficiency for solar hydrogen and peroxydisulfate production
Authors: Nakajima Tomohiko , Hagino Aya , Nakamura Takako , Tsuchiya Tetsuo , Sayama Kazuhiro
Published: November 2016

We prepared WO3 nanosponge photoanodes by nanoparticle/solution hybrid dispersion–deposition for production of “high-value-added” reagents.
Monolayer titanium carbide hollow sphere arrays formed via an atomic layer deposition assisted method and their excellent high-temperature supercapacitor performance
Authors: Zhong Yu , Xia Xinhui , Zhan Jiye , Wang Yadong , Wang Xiuli , Tu Jiangping
Published: November 2016

High-quality titanium carbide (TiC) hollow sphere arrays on a conductive substrate are fabricated, and a new type of organic symmetric supercapacitor is assembled that shows impressive capacitance at high temperatures.
Poly(3-hexylthiophene) (P3HT): fruit fly or outlier in organic solar cell research?
Authors: Kleinschmidt Andrew T. , Root Samuel E. , Lipomi Darren J.
Published: November 2016

Regioregular poly(3-hexylthiophene) (P3HT) is used as a model polymer for research in organic solar cells.
Efficient delivery of chlorin e6 into ovarian cancer cells with octalysine conjugated superparamagnetic iron oxide nanoparticles for effective photodynamic therapy
Authors: Zhao Li , Yang Hongkuan , Amano Tsukuru , Qin Hongmei , Zheng Luyi , Takahashi Akimasa , Zhao Shiguang , Tooyama Ikuo , Murakami Takashi , Komatsu Naoki
Published: November 2016

Chlorin e6, loaded on the surface of SPION-PG-Lys8 through electrostatic attraction, was delivered preferentially into mitochondria of SKOV3 ovarian cancer cells, improving efficacy of photodynamic therapy significantly.
Replacing the non-polarized CC bond with an isoelectronic polarized B–N unit for the design and development of smart materials
Authors: Neena Kalluvettukuzhy K. , Thilagar Pakkirisamy
Published: November 2016

By exploiting BN/CC isosterism, aggregation induced emission enhancement (AIEE) and mechanochromic features were realised in tetra-arylaminoboranes for the first time.
Voltage-gated sodium channels and pain-related disorders
Authors: Kanellopoulos Alexandros H. , Matsuyama Ayako
Published: November 2016

Voltage-gated sodium channels (VGSCs) are heteromeric transmembrane protein complexes. Nine homologous members, SCN1A–11A, make up the VGSC gene family. Sodium channel isoforms display a wide range of kinetic properties endowing different neuronal types with distinctly varied firing properties. Among the VGSCs isoforms, Nav1.7, Nav1.8 and Nav1.9 are preferentially expressed in the peripheral nervous system. These isoforms are known to be crucial in the conduction of nociceptive stimuli with mutations in these channels thought to be the underlying cause of a variety of heritable pain disorders. This review provides an overview of the current literature concerning the role of VGSCs in the generation of pain and heritable pain disorders.
Long non-coding RNAs (lncRNAs) in skeletal and cardiac muscle: potential therapeutic and diagnostic targets?
Authors: McMullen Julie R. , Drew Brian G.
Published: November 2016

The recent discovery that thousands of RNAs are transcribed by the cell but are never translated into protein, highlights a significant void in our current understanding of how transcriptional networks regulate cellular function. This is particularly astounding when we consider that over 75% of the human genome is transcribed into RNA, but only approximately 2% of RNA is translated into known proteins. This raises the question as to what function the other so-called ‘non-coding RNAs’ (ncRNAs) are performing in the cell. Over the last decade, an enormous amount of research has identified several classes of ncRNAs, predominantly short ncRNAs (<200 nt) that have been confirmed to have functional significance. Recent advances in sequencing technology and bioinformatics have also allowed for the identification of a novel class of ncRNAs, termed long ncRNA (lncRNA) (>200 nt). Several studies have recently shown that long non-coding RNAs (lncRNAs) are associated with tissue development and disease, particularly in cell types that undergo differentiation such as stem cells, cancer cells and striated muscle (skeletal/cardiac). Therefore, understanding the function of these lncRNAs and designing strategies to detect and manipulate them, may present novel therapeutic and diagnostic opportunities. This review will explore the current literature on lncRNAs in skeletal and cardiac muscle and discuss their recent implication in development and disease. Lastly, we will also explore the possibility of using lncRNAs as therapeutic and diagnostic tools and discuss the opportunities and potential shortcomings to these applications.
Consent, Refusal, and Waivers in Patient-Centered Dysphagia Care: Using Law, Ethics, and Evidence to Guide Clinical Practice
Authors: Horner Jennifer , Modayil Maria , Chapman Laura Roche , Dinh An
Published: November 2016

Purpose

When patients refuse medical or rehabilitation procedures, waivers of liability have been used to bar future lawsuits. The purpose of this tutorial is to review the myriad issues surrounding consent, refusal, and waivers. The larger goal is to invigorate clinical practice by providing clinicians with knowledge of ethics and law. This tutorial is for educational purposes only and does not constitute legal advice.

Method

The authors use a hypothetical case of a “noncompliant” individual under the care of an interdisciplinary neurorehabilitation team to illuminate the ethical and legal features of the patient–practitioner relationship; the elements of clinical decision-making capacity; the duty of disclosure and the right of informed consent or informed refusal; and the relationship among noncompliance, defensive practices, and iatrogenic harm. We explore the legal question of whether waivers of liability in the medical context are enforceable or unenforceable as a matter of public policy.

Conclusions

Speech-language pathologists, among other health care providers, have fiduciary and other ethical and legal obligations to patients. Because waivers try to shift liability for substandard care from health care providers to patients, courts usually find waivers of liability in the medical context unenforceable as a matter of public policy.
Shock-wave processing of C60 in hydrogen
Authors: Biennier L. , Jayaram V. , Suas-David N. , Georges R. , Singh M. Kiran , Arunan E. , Kassi S. , Dartois E. , Reddy K. P. J.
Published: November 2016

Context. Interstellar carbonaceous particles and molecules are subject to intense shocks in astrophysical environments. Shocks induce a rapid raise in temperature and density which strongly affects the chemical and physical properties of both the gas and solid phases of the interstellar matter.

Aims. The shock-induced thermal processing of C60 particles in hydrogen has been investigated in the laboratory under controlled conditions up to 3900 K with the help of a material shock-tube.

Methods. The solid residues generated by the exposure of a C60/H2 mixture to a millisecond shock wave were collected and analyzed using X-ray diffraction, scanning electron microscopy, transmission electron microscopy, Raman micro-spectroscopy, and infrared micro-spectroscopy. The gaseous products were analyzed by Gas Chromatography and Cavity Ring Down Spectroscopy.

Results. Volatile end-products appear above reflected shock gas temperatures of ~2540 K and reveal the substantial presence of small molecules with one or two C atoms. These observations confirm the role played by the C2 radical as a major product of C60 fragmentation and less expectedly highlight the existence of a single C atom loss channel. Molecules with more than two carbon atoms are not observed in the post-shock gas. The analysis of the solid component shows that C60 particles are rapidly converted into amorphous carbon with a number of aliphatic bridges.

Conclusions. The absence of aromatic CH stretches on the IR spectra indicates that H atoms do not link directly to aromatic cycles. The fast thermal processing of C60 in H2 over the 800–3400 K temperature range leads to amorphous carbon. The analysis hints at a collapse of the cage with the formation of a few aliphatic connections. A low amount of hydrogen is incorporated into the carbon material. This work extends the range of applications of shock tubes to studies of astrophysical interest.
Concentration-tuned interactions and structures in flowing suspensions under a gradient AC electric field
Authors: Tada Shigeru , Qiu Zhiyong , Shen Yan
Published: November 2016

In this study, numerical simulations of suspensions of Al2O3 particles in corn oil at various volume fractions were performed to explore the mechanisms involved in the electro-mechanical behavior of positive polarized particles suspended in an insulated suspending medium traveling through a rotating flow channel while exposed to a nonuniform AC electric field. A theoretical model was developed to simulate the trajectories of individual particles under the action of dielectrophoretic (DEP), dipole-dipole interparticle, viscous, and gravitational forces in a laminar flow. The results demonstrated that particles began to aggregate along the edges of electrodes with electric field application. New particles coming from more distant regions then gradually joined the vertices of particle aggregates, leading to the growth of chain-like clusters along the electric field gradient. Predictions showed good agreement with the results observed in a previous experiment. The new findings of this study are that the DEP force always tends to confine particles near the electrode edges, whereas the clustering of particles on the electrodes arises from the competition between particle interaction due to the DEP force and the long-range dipole-dipole interparticle interaction with neighboring particles. This process became more apparent with higher volume fractions of particle.
Effects of tillage on the soil water retention curve during a fallow period of a semiarid dryland
Authors: Peña-Sancho C. , López M. V. , Gracia R. , Moret-Fernández D.
Published: November 2016

Tillage practices have a significant influence on the soil hydro-physical properties. The objective of this work was to evaluate the effect of tillage on the α (a scaling factor) and n (a pore size distribution parameter) van Genuchten soil water retention curve parameters during an 18-month long fallow period in a semiarid dryland. Three different tillage systems employed during 23 years of trials were compared: conventional (CT), reduced (RT) and no-tillage (NT). Measurements of soil bulk density (ρb) and the soil water retention curve θ(ψ) were performed at 0–10, 10–20 and 20–30cm soil depths. The θ(ψ) was determined with the Time Domain Reflectometry (TDR)-pressure cells at the following pressure heads: 0.5, 1.5, 3, 10, 50, 100, 500 and 1500kPa. From these data, α, n and the SDexter index were evaluated. The 0–40cm depth soil volumetric water content, θ, was also measured in the field using the TDR technique. Compared with CT and RT, NT had the highest θ values during all the fallow period. No significant influence of soil depth on θ(ψ) was observed in all tillage treatments at each sampling date. Although under consolidated soil conditions no significant differences in ρb and the water content at saturation (θs) were observed among tillage treatments, NT had the highest and lowest values of ρb and θs, respectively. The loosening of soil due to tillage practices in CT and RT significantly decreased ρb and increased θ at the wet-end section of θ(ψ). Post-tillage rainfall resulted in significant decreases in θs, α and the maximum value of the pore size distribution (PSDmax). The different soil structure created by mouldboard ploughing (CT) and chiselling (RT) explained the higher PSDmax under RT than CT. The most important changes in θ(ψ) followed the first copious effective rainfall events (>10mm) after tillage. These facts enabled the soil to recover the pre-tillage water retention curve shapes and the van Genuchten parameters pre-tillage values. Effective rainfall events in the late fallow had a minor effect on the water retention curve. Although tillage tended to increase n, this change was not significant. The SDexter index, which was also affected by tillage, was greater than 0.035 during all the fallow period, indicating good soil physical quality.
Early warning signals of regime shifts in coupled human–environment systems
Authors: Bauch Chris T. , Sigdel Ram , Pharaon Joe , Anand Madhur
Published: November 2016

In complex systems, a critical transition is a shift in a system’s dynamical regime from its current state to a strongly contrasting state as external conditions move beyond a tipping point. These transitions are often preceded by characteristic early warning signals such as increased system variability. However, early warning signals in complex, coupled human–environment systems (HESs) remain little studied. Here, we compare critical transitions and their early warning signals in a coupled HES model to an equivalent environment model uncoupled from the human system. We parameterize the HES model, using social and ecological data from old-growth forests in Oregon. We find that the coupled HES exhibits a richer variety of dynamics and regime shifts than the uncoupled environment system. Moreover, the early warning signals in the coupled HES can be ambiguous, heralding either an era of ecosystem conservationism or collapse of both forest ecosystems and conservationism. The presence of human feedback in the coupled HES can also mitigate the early warning signal, making it more difficult to detect the oncoming regime shift. We furthermore show how the coupled HES can be “doomed to criticality”: Strategic human interactions cause the system to remain perpetually in the vicinity of a collapse threshold, as humans become complacent when the resource seems protected but respond rapidly when it is under immediate threat. We conclude that the opportunities, benefits, and challenges of modeling regime shifts and early warning signals in coupled HESs merit further research.
Evidential fictive interaction (in Ungarinyin and Russian)
Authors: Spronck Stef
Published: November 2016

This chapter introduces and examines the notion of “evidential fictive participants” and their grammatical expression in utterances of fictive interaction. It focuses on fictive direct speech constructions and draws on examples from the Australian Aboriginal language Ungarinyin and Russian. After presenting data from these languages the chapter suggests that through the notion of participants fictive interaction forms a framework for grammatical typology. This framework has both a strong philosophical and analytical foundation and allows for an integrated approach to grammatical categories based on their relation to the conversation frame.
Echolalia as communicative strategy
Authors: Dornelas Aline , Pascual Esther
Published: November 2016

We explore how fictive interaction (Pascual 2002, 2014), manifested as echolalia (i.e. prior speech repeated verbatim), is successfully used by autistic children as a compensatory strategy in conversation. We video-recorded four Brazilian autistic children between the ages of 4 and 12 in interactions with adults in weekly therapy sessions. We found that these autistic children do not use direct speech to represent prior speech only, as in ordinary reported speech. Instead, they use direct speech to make mental contact with past (types of) communicative situations. Reenactment is used fictively as a means of expressing needs, describing situations, and referring to people, animals, and events. These fictive quotations may reflect socio-communicative or socio-cultural knowledge, or experiences with prior specific interactions.
Reflections on translators and authors
Authors: Rosenwald Lawrence
Published: November 2016

Reflections of three sorts on the relations between translators and authors: autobiographical, polemical, and historical. The autobiographical reflections focus on the relation between the author and the German novelist Jeannette Lander and between the author and the German-Jewish philosopher Franz Rosenzweig. The polemical reflections call into question the notion that the translation is of less value than the original, the translator a lesser writer than the author. The historical reflections focus on the history of translating Yiddish into English in America.
A prospective examination of the impact of high levels of exercise training on sedentary behaviour
Authors: Swartz Ann M. , Miller Nora E. , Cho Young IK , Welch Whitney A. , Strath Scott J.
Published: November 2016

The aim of this study is to determine changes in sedentary behaviour in response to extensive aerobic exercise training. Participants included adults who self‐selected to run a marathon. Sedentary behaviour, total activity counts and physical activity (PA) intensity were assessed (Actigraph GT3X) for seven consecutive days during seven assessment periods (−3, −2, and −1 month prior to the marathon, within 2 weeks of the marathon, and +1, +2, and +3 months after the marathon). Models were fitted with multiple imputation data using the STATA mi module. Random intercept generalized least squares (GLS) regression models were used to determine change in sedentary behaviour with seven waves of repeated measures. Results: Twenty‐three individuals (mean ± Sx: 34.4 ± 2.1y, 23.0 ± 1.9% fat, 15 women, 8 men) completed the study. Marathon finishing times ranged from 185 to 344 minutes (253.2 ± 9.6 minutes). Total counts in the vertical axis were 1,729,414 lower one month after the race, compared with two months prior to the race (peak training). Furthermore, counts per minute decreased by 252.7 counts·minute−1 during that same time period. Daily sedentary behaviour did not change over the seven assessment periods, after accounting for age, gender, per cent body fat, wear time, marathon finishing time, and previous marathon experience. This prospective study supports the notion that PA and sedentary behaviours are distinct, showing that sedentary behaviour was not impacted by high levels of aerobic training.
Evidence for a confidence–accuracy relationship in memory for same- and cross-race faces
Authors: Nguyen Thao B. , Pezdek Kathy , Wixted John T.
Published: November 2016

Discrimination accuracy is usually higher for same- than for cross-race faces, a phenomenon known as the cross-race effect (CRE). According to prior research, the CRE occurs because memories for same- and cross-race faces rely on qualitatively different processes. However, according to a continuous dual-process model of recognition memory, memories that rely on qualitatively different processes do not differ in recognition accuracy when confidence is equated. Thus, although there are differences in overall same- and cross-race discrimination accuracy, confidence-specific accuracy (i.e., recognition accuracy at a particular level of confidence) may not differ. We analysed datasets from four recognition memory studies on same- and cross-race faces to test this hypothesis. Confidence ratings reliably predicted recognition accuracy when performance was above chance levels (Experiments 1, 2, and 3) but not when performance was at chance levels (Experiment 4). Furthermore, at each level of confidence, confidence-specific accuracy for same- and cross-race faces did not significantly differ when overall performance was above chance levels (Experiments 1, 2, and 3) but significantly differed when overall performance was at chance levels (Experiment 4). Thus, under certain conditions, high-confidence same-race and cross-race identifications may be equally reliable.
Crime reporting as storytelling in Persian/Farsi news journalism – perspectives on the narrative function
Authors: White P.R.R. , Makki Mohammad
Published: November 2016

This paper is concerned with the nature of storytelling and how different types of story or narrative might be classified and characterised by reference to their generic structures and ultimate social functions. More specifically, it is concerned with Persian/Farsi-language reports of crimes in Iranian newspapers. It describes and analyses the various ways in which these texts are organised structurally, informationally and with respect to “newsworthiness”, the various ways in which they deal with chronological sequence and the various ways in which they position the reader attitudinally vis-à-vis the events described and/or their protagonists. In so doing, it provides insights into the similarities and differences between these instances of Persian/Farsi journalism and what the journalism studies literature has presented as “typical” of modern news reports in English and other languages. It also provides insights into the nature of these Iranian crime reports as instances of storytelling or narrative, proposing that taxonomies of the different subtypes of storytelling outlined in the Sydney Genre School literature should be refined to accommodate the modes of storytelling observed in the authors’ data set of crime reports.
SPADEVizR: an R package for visualization, analysis and integration of SPADE results
Authors: Gautreau Guillaume , Pejoski David , Le Grand Roger , Cosma Antonio , Beignon Anne-Sophie , Tchitchek Nicolas
Published: November 2016

Motivation

Flow, hyperspectral and mass cytometry are experimental techniques measuring cell marker expressions at the single cell level. The recent increase of the number of markers simultaneously measurable has led to the development of new automatic gating algorithms. Especially, the SPADE algorithm has been proposed as a novel way to identify clusters of cells having similar phenotypes in high-dimensional cytometry data. While SPADE or other cell clustering algorithms are powerful approaches, complementary analysis features are needed to better characterize the identified cell clusters.

Results

We have developed SPADEVizR, an R package designed for the visualization, analysis and integration of cell clustering results. The available statistical methods allow highlighting cell clusters with relevant biological behaviors or integrating them with additional biological variables. Moreover, several visualization methods are available to better characterize the cell clusters, such as volcano plots, streamgraphs, parallel coordinates, heatmaps, or distograms. SPADEVizR can also generate linear, Cox or random forest models to predict biological outcomes, based on the cell cluster abundances. Additionally, SPADEVizR has several features allowing to quantify and to visualize the quality of the cell clustering results. These analysis features are essential to better interpret the behaviors and phenotypes of the identiﬁed cell clusters. Importantly, SPADEVizR can handle clustering results from other algorithms than SPADE.

Availability and Implementation

SPADEVizR is distributed under the GPL-3 license and is available at https://github.com/tchitchek-lab/SPADEVizR.

Supplementary information

Supplementary data are available at Bioinformatics online.
Combined effects of elevated pCO2, temperature, and starvation stress on larvae of a large tropical marine fish
Authors: Bignami Sean , Sponaugle Su , Hauff Martha , Cowen Robert K.
Published: November 2016

Ocean acidification and other environmental changes pose an ecological challenge to marine organisms globally. Although the youngest life stages of these organism are likely to be most affected, a limited number of studies of larval fishes have investigated the effects of combined stressors. We conducted two experiments on larval cobia (Rachycentron canadum) raised under combinations of elevated pCO2 and increased temperature or starvation stress. Larvae responded to individual CO2, temperature, and rationing treatments, and there was a negative effect of elevated pCO2 on starvation resistance, but few synergistic effects of combined stressors. Elevated pCO2 (1700–2100 μatm pCO2) caused a transient but significant reduction in larval standard length (SL), growth rate, and development rate, while warmer temperature (32 vs. 27 °C) caused a consistent increase in SL, development rate, and swimming ability. Larval condition (RNA:DNA ratio) was unaffected by elevated pCO2 although larvae fed a 25% ration had significantly reduced SL, growth rate, and development rate. Under complete feeding cessation, larvae in elevated-pCO2 seawater demonstrated lower starvation resistance, indicating that acidification may increase starvation risk in a patchy marine environment. Overall, our results indicate that larval cobia are resistant to any major direct impact of combined elevated pCO2 and temperature or rationing stress.
A flat-spectrum candidate for a track-type high-energy neutrino emission event, the case of blazar PKS 0723−008
Authors: Kun E. , Biermann P. L. , Gergely L. Á.
Published: November 2016

By cross-correlating both the Parkes Catalogue and the Second Planck Catalogue of Compact Sources with the arrival direction of the track-type neutrinos detected by the IceCube Neutrino Observatory, we find the flat-spectrum blazar PKS 0723−008 as a good candidate for the high-energy neutrino event 5 (ID5). Apart from its coordinates matching those of ID5, PKS 0723−008 exhibits further interesting radio properties. Its spectrum is flat up to high Planck frequencies, and it produced a fivefold-increased radio flux density through the last decade. Based upon these radio properties we propose a scenario of binary black hole evolution leading to the observed high-energy neutrino emission. The main contributing events are the spin-flip of the dominant black hole, the formation of a new jet with significant particle acceleration and interaction with the surrounding material, with the corresponding increased radio flux. Doppler boosting from the underlying jet pointing to the Earth makes it possible to identify the origin of the neutrinos, so the merger itself is the form of an extended flat-spectrum radio emission, a key selection criterion to find traces of this complex process.