bluuebunny/crossref_metadata_2025 huggingface dataset:
On the length scales of hypersonic shock-induced large separation bubbles near leading edges
Authors: Sriram R. , Srinath L. , Devaraj Manoj Kumar K. , Jagadeesh G.
Published: September 2016

The interaction of a hypersonic boundary layer on a flat plate with an impinging shock – an order of magnitude stronger than that required for incipient separation of the boundary layer – near sharp and blunt leading edges (with different bluntness radii from 2 to 6 mm) is investigated experimentally, complemented by numerical computations. The resultant separation bubble is of length comparable to the distance of shock impingement from the leading edge, rather than the boundary layer thickness at separation; it is termed large separation bubble. Experiments are performed in the IISc hypersonic shock tunnel HST-2 at nominal Mach numbers 5.88 and 8.54, with total enthalpies 1.26 and $1.85~\text{MJ}~\text{kg}^{-1}$ respectively. Schlieren flow visualization using a high-speed camera and surface pressure measurements using fast response sensors are the diagnostics. For the sharp leading edge case, the separation length was found to follow an inviscid scaling law according to which the scaled separation length $(L_{sep}/x_{r})M_{er}^{3}$ is found to be linearly related to the reattachment pressure ratio $p_{r}/p_{er}$; where $L_{sep}$ is the measured separation length, $x_{r}$ the distance of reattachment from the leading edge, $M$ the Mach number, $p$ the static pressure and the subscripts $r$ and $e$ denote the conditions at the reattachment location and at the edge of the boundary layer at the shock impingement location respectively. However, for all the blunt leading edges $(L_{sep}/x_{r})M_{er}^{3}$ was found to be a constant irrespective of Mach number and much smaller than the sharp leading edge cases. The possible contributions of viscous and non-viscous mechanisms towards the observed phenomena are explored.
On the errors involved in ice-thickness estimates II: errors in digital elevation models of ice thickness
Authors: LAPAZARAN J. J. , OTERO J. , MARTÍN-ESPAÑOL A. , NAVARRO F. J.
Published: September 2016

This paper is the second (Paper II) in a set of studies concerning the errors involved in the estimate of ice thickness and ice volume. Here we present a detailed analysis of the errors involved in the generation of ice-thickness DEMs constructed, most often, from GPR data, complemented by boundary data and sometimes, additional synthetic data arising from estimates based on theoretical considerations supported by independent data. We describe a complete methodology of error analysis that, starting from the errors in the data, propagates them to the grid nodes. In turn, the interpolation error at the grid nodes is calculated using a novel procedure that also provides an estimate of the bias introduced by the interpolation process. Finally, both errors are combined at the grid nodes to produce a gridpoint-dependent error estimate, which is complemented by an overall error estimate providing an assessment of the quality of the DEM. This methodology is illustrated with the case study of Werenskioldbreen, a land-terminating polythermal glacier in Svalbard.
SINCERITY, HYPOCRISY, AND CONSPIRACY THEORY IN THE OCCUPIED PALESTINIAN TERRITORY
Authors: Allen Lori
Published: September 2016

Concerns about lying and sincerity in politics are common in most societies, as are concerns about conspiracy theories. But in the occupied Palestinian territory, these concerns give rise to particular kinds of effects because of the conditions of Israeli occupation. Political theorists often interpret opacity claims and conspiracy theories as responses to social disorder. In occupied Palestine, disorder and instability are standard. Opacity claims and conspiracy theories therefore require a different kind of analysis. Through an examination of the semiotic ideology of sincerity, especially as it has emerged in the conflict between Fatah and Hamas, this article argues that opacity claims act as a form of nationalist pedagogy, at once reinforcing the basic principles of sincerity of action and word, and encouraging a wariness of political spin.
The View from the Edge: The Indian Ocean's Middle East
Authors: Green Nile
Published: September 2016

I first encountered the Indian Ocean on the shores of Makran. I thought I was at land's end, Asia's edge. The ocean hadn't entered my thoughts except asnon plus ultra, an ending void. The map said Baluchistan, and I had come to find the Baluch. But I soon found Africans and Zikris, palm-frond huts and Omani passports, old soldiers (or mercenaries) from an overseas foreign legion and smugglers of whiskey, opium, and pharmaceuticals. Now China has built a port there; then, less than twenty years ago, they were still making dhows, subtle smuggling ships. Yet it was far from romantic. It was a rough and hard place where traders and fishers eked a marginal existence from the watery edge of a dust-powder desert. Karachi was thirty-six hours by bus then truck. But Pakistan was an abstract and suspect idea; locals talked more of Muscat. A year or two later, in the Tihama of Yemen, I watched as boatloads of Africans (refugees? job hunters? all men at any rate) ran ashore through the surf. My Arab colleagues, all from the highlands, said they arrived every day, and spoke ill of them. A while after that, in Muscat, I listened with curiosity to Arabic laced with Urdu (or was it Hindi, or Gujarati? They were just nouns,Wanderwörter: terms that travel). In Iran, it was different sounds of the ocean I heard when urban friends gave me tapes ofbandarī, the music of the ports.
Sindbad's Ocean: Reframing the Market in the Middle East
Authors: Mathew Johan
Published: September 2016

There are few figures as universally beloved and yet recognizably “Middle Eastern” as Sindbad. The text of Sindbad's seven voyages travel easily across continents and languages and many of the tales blur imperceptibly into those of Homer'sThe Odysseyand Swift'sGulliver's Travels. Yet this swashbuckling adventurer is also firmly situated in the world of Abbasid Iraqandthe Indian Ocean world. Sindbad is clearly identified as a good Muslim and respected Baghdadi merchant, and while fantastical, there are recognizable geographic and cultural markers that locate his voyages within the Indian Ocean world. This iconic character of Arab popular culture pushes us to contemplate how easily the Arab world flows into that of the Indian Ocean.
Multiple Mobilities, Multiple Sovereignties, Multiple Speeds: Exploring Maritime Connections in the Age of Empire
Authors: Huber Valeska
Published: September 2016

What can we gain by looking at maritime spaces? Does this enable us to work towards a global history of the Middle East that moves beyond at times arbitrary geographical and disciplinary borders? In this essay I argue that maritime spaces might be particularly suitable for exploring the boundaries of Middle East studies and their interconnection with global history. By implication, the study of Middle Eastern maritime connections might be especially well fitted to develop new and more complex global histories. To make this point, a specific and perhaps unusual maritime site in the Middle East will be assessed. The Suez Canal opened in 1869 and quickly turned into a major artery of traffic between Europe on the one side, and Asia, East Africa, and Australia on the other. More importantly for our purposes, it is located at the very heart of the Middle East, where Africa and Asia, the Mediterranean and the Red Sea (and with it the Indian Ocean world), and water and desert intersect.
Geographic Information Systems (GIS) in International Relations
Authors: Branch Jordan
Published: September 2016

Geographic Information Systems (GIS) are being applied with increasing frequency, and with increasing sophistication, in international relations and in political science more generally. Their benefits have been impressive: analyses that simply would not have been possible without GIS are now being completed, and the spatial component of international politics—long considered central but rarely incorporated analytically—has been given new emphasis. However, new methods face new challenges, and to apply GIS successfully, two specific issues need to be addressed: measurement validity and selection bias. Both relate to the challenge of conceptualizing nonspatial phenomena with the spatial tools of GIS. Significant measurement error can occur when the concepts that are coded as spatial variables are not, in fact, validly measured by the default data structure of GIS, and selection bias can arise when GIS systematically excludes certain types of units. Because these potential problems are hidden by the technical details of the method, GIS data sets and analyses can sometimes appear to overcome these challenges when, in fact, they fail to do so. Once these issues come to light, however, potential solutions become apparent—including some in existing applications in international relations and in other fields.
Insight from animal models of environmentally driven epigenetic changes in the developing and adult brain
Authors: Doherty Tiffany S. , Roth Tania L.
Published: September 2016

The efforts of many neuroscientists are directed toward understanding the appreciable plasticity of the brain and behavior. In recent years, epigenetics has become a core of this focus as a prime mechanistic candidate for behavioral modifications. Animal models have been instrumental in advancing our understanding of environmentally driven changes to the epigenome in the developing and adult brain. This review focuses mainly on such discoveries driven by adverse environments along with their associated behavioral outcomes. While much of the evidence discussed focuses on epigenetics within the central nervous system, several peripheral studies in humans who have experienced significant adversity are also highlighted. As we continue to unravel the link between epigenetics and phenotype, discerning the complexity and specificity of epigenetic changes induced by environments is an important step toward understanding optimal development and how to prevent or ameliorate behavioral deficits bred by disruptive environments.
Genome-wide DNA methylation in 1-year-old infants of mothers with major depressive disorder
Authors: Cicchetti Dante , Hetzel Susan , Rogosch Fred A. , Handley Elizabeth D. , Toth Sheree L.
Published: September 2016

A genome-wide methylation study was conducted among a sample of 114 infants (M age = 13.2 months, SD = 1.08) of low-income urban women with (n = 73) and without (n = 41) major depressive disorder. The Illumina HumanMethylation450 BeadChip array with a GenomeStudio Methylation Module and Illumina Custom model were used to conduct differential methylation analyses. Using the 5.0 × 10–7p value, 2,119 loci were found to be significantly different between infants of depressed and nondepressed mothers. Infants of depressed mothers had greater methylation at low methylation sites (0%–29%) compared to infants of nondepressed mothers. At high levels of methylation (70%–100%), the infants of depressed mothers were predominantly hypomethylated. The mean difference in methylation between the infants of depressed and infants of nondepressed mothers was 5.23%. Disease by biomarker analyses were also conducted using GeneGo MetaCore Software. The results indicated significant cancer-related differences in biomarker networks such as prostatic neoplasms, ovarian and breast neoplasms, and colonic neoplasms. The results of a process networks analysis indicated significant differences in process networks associated with neuronal development and central nervous system functioning, as well as cardiac development between infants of depressed and nondepressed mothers. These findings indicate that early in development, infants of mothers with major depressive disorder evince epigenetic differences relative to infants of well mothers that suggest risk for later adverse health outcomes.
THE VALUE OF UNHAPPINESS
Authors: Vitrano Christine
Published: September 2016

John Stuart Mill famously remarked that it is ‘better to be Socrates dissatisfied than a fool satisfied’.1 But is it necessarily better to be Socrates satisfied than Socrates dissatisfied?
Constraints, competition, and competitiveness: explaining the non-linear effect of democratization on political budget cycles
Authors: Eibl Ferdinand , Lynge Halfdan
Published: September 2016

The literature on political budget cycles (PBCs) does not offer a full-fledged theory about the effect of democratization. However, it does imply a non-linear effect along the regime spectrum: positive at the autocratic end, negative at the democratic end. We theoretically develop and empirically test this implication by pointing to two countervailing effects of democratization:executive constraintsandpolitical competition. While the former contains PBCs, the latter stimulates them. Because of their empirical covariation, PBCs occur primarily in hybrid regimes where the decision-making powers of the executive are relatively unrestricted and politics is relatively competitive. We also show that while executive constraints and political competition condition PBCs, what triggers the fluctuations iselectoral competitiveness. Only when incumbents fear electoral defeat, do they create PBCs. The study is based on novel data on public spending in 112 countries, covering the entire regime spectrum over the period from 1960 to 2006.
First Arctic Science Ministers' Confab Yields Cooperation Pledge
Authors: Showstack Randy
Published: September 2016

Newly announced ventures and advances include developing an Integrated Arctic Observing System and the release of the first-ever Arctic-wide digital elevation model.
An endoplasmic reticulum stress-regulated lncRNA hosting a microRNA megacluster induces early features of diabetic nephropathy
Authors: Kato Mitsuo , Wang Mei , Chen Zhuo , Bhatt Kirti , Oh Hyung Jung , Lanting Linda , Deshpande Supriya , Jia Ye , Lai Jennifer Y.C. , O’Connor Christopher L. , Wu YiFan , Hodgin Jeffrey B. , Nelson Robert G. , Bitzer Markus , Natarajan Rama
Published: September 2016

It is important to find better treatments for diabetic nephropathy (DN), a debilitating renal complication. Targeting early features of DN, including renal extracellular matrix accumulation (ECM) and glomerular hypertrophy, can prevent disease progression. Here we show that a megacluster of nearly 40 microRNAs and their host long non-coding RNA transcript (lnc-MGC) are coordinately increased in the glomeruli of mouse models of DN, and mesangial cells treated with transforming growth factor-β1 (TGF- β1) or high glucose. Lnc-MGC is regulated by an endoplasmic reticulum (ER) stress-related transcription factor, CHOP. Cluster microRNAs and lnc-MGC are decreased in diabeticChop−/−mice that showed protection from DN. Target genes of megacluster microRNAs have functions related to protein synthesis and ER stress. A chemically modified oligonucleotide targeting lnc-MGC inhibits cluster microRNAs, glomerular ECM and hypertrophy in diabetic mice. Relevance to human DN is also demonstrated. These results demonstrate the translational implications of targeting lnc-MGC for controlling DN progression.
Single-molecule visualization of dynamic transitions of pore-forming peptides among multiple transmembrane positions
Authors: Li Ying , Qian Zhenyu , Ma Li , Hu Shuxin , Nong Daguan , Xu Chunhua , Ye Fangfu , Lu Ying , Wei Guanghong , Li Ming
Published: September 2016

Research on the dynamics of single-membrane proteins remains underdeveloped due to the lack of proper approaches that can probe in real time the protein’s insertion depth in lipid bilayers. Here we report a single-molecule visualization method to track both vertical insertion and lateral diffusion of membrane proteins in supported lipid bilayers by exploiting the surface-induced fluorescence attenuation (SIFA) of fluorophores. The attenuation follows a d−4 dependency, where d is the fluorophore-to-surface distance. The method is validated by observing the antimicrobial peptide LL-37 to transfer among five transmembrane positions: the surface, the upper leaflet, the centre, the lower leaflet and the bottom of the lipid bilayer. These results demonstrate the power of SIFA to study protein-membrane interactions and provide unprecedented in-depth understanding of molecular mechanisms of the insertion and translocation of membrane proteins.
Chemotaxis towards autoinducer 2 mediates autoaggregation in Escherichia coli
Authors: Laganenka Leanid , Colin Remy , Sourjik Victor
Published: September 2016

Bacteria communicate by producing and sensing extracellular signal molecules called autoinducers. Such intercellular signalling, known as quorum sensing, allows bacteria to coordinate and synchronize behavioural responses at high cell densities. Autoinducer 2 (AI-2) is the only known quorum-sensing molecule produced by Escherichia coli but its physiological role remains elusive, although it is known to regulate biofilm formation and virulence in other bacterial species. Here we show that chemotaxis towards self-produced AI-2 can mediate collective behaviour—autoaggregation—of E. coli. Autoaggregation requires motility and is strongly enhanced by chemotaxis to AI-2 at physiological cell densities. These effects are observed regardless whether cell–cell interactions under particular growth conditions are mediated by the major E. coli adhesin (antigen 43) or by curli fibres. Furthermore, AI-2-dependent autoaggregation enhances bacterial stress resistance and promotes biofilm formation.
Nonlinear optical observation of coherent acoustic Dirac plasmons in thin-film topological insulators
Authors: Glinka Yuri D. , Babakiray Sercan , Johnson Trent A. , Holcomb Mikel B. , Lederman David
Published: September 2016

Low-energy collective electronic excitations exhibiting sound-like linear dispersion have been intensively studied both experimentally and theoretically for a long time. However, coherent acoustic plasmon modes appearing in time-domain measurements are rarely observed due to Landau damping by the single-particle continua. Here we report on the observation of coherent acoustic Dirac plasmon (CADP) modes excited in indirectly (electrostatically) opposite-surface coupled films of the topological insulator Bi2Se3. Using transient second-harmonic generation, a technique capable of independently monitoring the in-plane and out-of-plane electron dynamics in the films, the GHz-range oscillations were observed without corresponding oscillations in the transient reflectivity. These oscillations were assigned to the transverse magnetic and transverse electric guided CADP modes induced by the evanescent guided Lamb acoustic waves and remained Landau undamped due to fermion tunnelling between the opposite-surface Dirac states.
The Architecture of the Cytoplasmic Region of Type III Secretion Systems
Authors: Makino Fumiaki , Shen Dakang , Kajimura Naoko , Kawamoto Akihiro , Pissaridou Panayiota , Oswin Henry , Pain Maria , Murillo Isabel , Namba Keiichi , Blocker Ariel J.
Published: September 2016

Type III secretion systems (T3SSs) are essential devices in the virulence of many Gram-negative bacterial pathogens. They mediate injection of protein effectors of virulence from bacteria into eukaryotic host cells to manipulate them during infection. T3SSs involved in virulence (vT3SSs) are evolutionarily related to bacterial flagellar protein export apparatuses (fT3SSs), which are essential for flagellar assembly and cell motility. The structure of the external and transmembrane parts of both fT3SS and vT3SS is increasingly well-defined. However, the arrangement of their cytoplasmic and inner membrane export apparatuses is much less clear. Here we compare the architecture of the cytoplasmic regions of the vT3SSs of Shigella flexneri and the vT3SS and fT3SS of Salmonella enterica serovar Typhimurium at ~5 and ~4 nm resolution using electron cryotomography and subtomogram averaging. We show that the cytoplasmic regions of vT3SSs display conserved six-fold symmetric features including pods, linkers and an ATPase complex, while fT3SSs probably only display six-fold symmetry in their ATPase region. We also identify other morphological differences between vT3SSs and fT3SSs, such as relative disposition of their inner membrane-attached export platform, C-ring/pods and ATPase complex. Finally, using classification, we find that both types of apparatuses can loose elements of their cytoplasmic region, which may therefore be dynamic.
Process-based design of dynamical biological systems
Authors: Tanevski Jovan , Todorovski Ljupčo , Džeroski Sašo
Published: September 2016

The computational design of dynamical systems is an important emerging task in synthetic biology. Given desired properties of the behaviour of a dynamical system, the task of design is to build an in-silico model of a system whose simulated be- haviour meets these properties. We introduce a new, process-based, design methodology for addressing this task. The new methodology combines a flexible process-based formalism for specifying the space of candidate designs with multi-objective optimization approaches for selecting the most appropriate among these candidates. We demonstrate that the methodology is general enough to both formulate and solve tasks of designing deterministic and stochastic systems, successfully reproducing plausible designs reported in previous studies and proposing new designs that meet the design criteria, but have not been previously considered.
A powerful weighted statistic for detecting group differences of directed biological networks
Authors: Yuan Zhongshang , Ji Jiadong , Zhang Xiaoshuai , Xu Jing , Ma Daoxin , Xue Fuzhong
Published: September 2016

Complex disease is largely determined by a number of biomolecules interwoven into networks, rather than a single biomolecule. Different physiological conditions such as cases and controls may manifest as different networks. Statistical comparison between biological networks can provide not only new insight into the disease mechanism but statistical guidance for drug development. However, the methods developed in previous studies are inadequate to capture the changes in both the nodes and edges and often ignore the network structure. In this study, we present a powerful weighted statistical test for group differences of directed biological networks, which is independent of the network attributes and can capture the changes in both the nodes and edges, as well as simultaneously accounting for the network structure through putting more weights on the difference of nodes locating on relatively more important position. Simulation studies illustrate that this method had better performance than previous ones under various sample sizes and network structures. One application to GWAS of leprosy successfully identifies the specific gene interaction network contributing to leprosy. Another real data analysis significantly identifies a new biological network, which is related to acute myeloid leukemia. One potential network responsible for lung cancer has also been significantly detected. The source R code is available on our website.
Phase-matched second harmonic generation with on-chip GaN-on-Si microdisks
Authors: Roland I. , Gromovyi M. , Zeng Y. , El Kurdi M. , Sauvage S. , Brimont C. , Guillet T. , Gayral B. , Semond F. , Duboz J. Y. , de Micheli M. , Checoury X. , Boucaud P.
Published: September 2016

We demonstrate phase-matched second harmonic generation in gallium nitride on silicon microdisks. The microdisks are integrated with side-coupling bus waveguides in a two-dimensional photonic circuit. The second harmonic generation is excited with a continuous wave laser in the telecom band. By fabricating a series of microdisks with diameters varying by steps of 8 nm, we obtain a tuning of the whispering gallery mode resonances for the fundamental and harmonic waves. Phase matching is obtained when both resonances are matched with modes satisfying the conservation of orbital momentum, which leads to a pronounced enhancement of frequency conversion.
Increased GABAB receptor signaling in a rat model for schizophrenia
Authors: Selten Martijn M. , Meyer Francisca , Ba Wei , Vallès Astrid , Maas Dorien A. , Negwer Moritz , Eijsink Vivian D. , van Vugt Ruben W. M. , van Hulten Josephus A. , van Bakel Nick H. M. , Roosen Joey , van der Linden Robert J. , Schubert Dirk , Verheij Michel M. M. , Kasri Nael Nadif , Martens Gerard J. M.
Published: September 2016

Schizophrenia is a complex disorder that affects cognitive function and has been linked, both in patients and animal models, to dysfunction of the GABAergic system. However, the pathophysiological consequences of this dysfunction are not well understood. Here, we examined the GABAergic system in an animal model displaying schizophrenia-relevant features, the apomorphine-susceptible (APO-SUS) rat and its phenotypic counterpart, the apomorphine-unsusceptible (APO-UNSUS) rat at postnatal day 20–22. We found changes in the expression of the GABA-synthesizing enzyme GAD67 specifically in the prelimbic- but not the infralimbic region of the medial prefrontal cortex (mPFC), indicative of reduced inhibitory function in this region in APO-SUS rats. While we did not observe changes in basal synaptic transmission onto LII/III pyramidal cells in the mPFC of APO-SUS compared to APO-UNSUS rats, we report reduced paired-pulse ratios at longer inter-stimulus intervals. The GABAB receptor antagonist CGP 55845 abolished this reduction, indicating that the decreased paired-pulse ratio was caused by increased GABAB signaling. Consistently, we find an increased expression of the GABAB1 receptor subunit in APO-SUS rats. Our data provide physiological evidence for increased presynaptic GABAB signaling in the mPFC of APO-SUS rats, further supporting an important role for the GABAergic system in the pathophysiology of schizophrenia.
Adhesive ligand tether length affects the size and length of focal adhesions and influences cell spreading and attachment
Authors: Attwood Simon J. , Cortes Ernesto , Haining Alexander William M. , Robinson Benjamin , Li Danyang , Gautrot Julien , del Río Hernández Armando
Published: September 2016

Cells are known to respond to physical cues from their microenvironment such as matrix rigidity. Discrete adhesive ligands within flexible strands of fibronectin connect cell surface integrins to the broader extracellular matrix and are thought to mediate mechanosensing through the cytoskeleton-integrin-ECM linkage. We set out to determine if adhesive ligand tether length is another physical cue that cells can sense. Substrates were covalently modified with adhesive arginylglycylaspartic acid (RGD) ligands coupled with short (9.5 nm), medium (38.2 nm) and long (318 nm) length inert polyethylene glycol tethers. The size and length of focal adhesions of human foreskin fibroblasts gradually decreased from short to long tethers. Furthermore, we found cell adhesion varies in a linker length dependent manner with a remarkable 75% reduction in the density of cells on the surface and a 50% reduction in cell area between the shortest and longest linkers. We also report the interplay between RGD ligand concentration and tether length in determining cellular spread area. Our findings show that without varying substrate rigidity or ligand density, tether length alone can modulate cellular behaviour.
BEN domain protein Elba2 can functionally substitute for linker histone H1 in Drosophila in vivo
Authors: Xu Na , Lu Xingwu , Kavi Harsh , Emelyanov Alexander V. , Bernardo Travis J. , Vershilova Elena , Skoultchi Arthur I. , Fyodorov Dmitry V.
Published: September 2016

Metazoan linker histones are essential for development and play crucial roles in organization of chromatin, modification of epigenetic states and regulation of genetic activity. Vertebrates express multiple linker histone H1 isoforms, which may function redundantly. In contrast, H1 isoforms are not present in Dipterans, including D. melanogaster, except for an embryo-specific, distantly related dBigH1. Here we show that Drosophila BEN domain protein Elba2, which is expressed in early embryos and was hypothesized to have insulator-specific functions, can compensate for the loss of H1 in vivo. Although the Elba2 gene is not essential, its mutation causes a disruption of normal internucleosomal spacing of chromatin and reduced nuclear compaction in syncytial embryos. Elba2 protein is distributed ubiquitously in polytene chromosomes and strongly colocalizes with H1. In H1-depleted animals, ectopic expression of Elba2 rescues the increased lethality and ameliorates abnormalities of chromosome architecture and heterochromatin functions. We also demonstrate that ectopic expression of BigH1 similarly complements the deficiency of H1 protein. Thus, in organisms that do not express redundant H1 isoforms, the structural and biological functions performed by canonical linker histones in later development, may be shared in early embryos by weakly homologous proteins, such as BigH1, or even unrelated, non-homologous proteins, such as Elba2.
Colluvium supply in humid regions limits the frequency of storm-triggered landslides
Authors: Parker Robert N. , Hales Tristram C. , Mudd Simon M. , Grieve Stuart W. D. , Constantine José A.
Published: September 2016

Shallow landslides, triggered by extreme rainfall, are a significant hazard in mountainous landscapes. The hazard posed by shallow landslides depends on the availability and strength of colluvial material in landslide source areas and the frequency and intensity of extreme rainfall events. Here we investigate how the time taken to accumulate colluvium affects landslide triggering rate in the Southern Appalachian Mountains, USA and how this may affect future landslide hazards. We calculated the failure potential of 283 hollows by comparing colluvium depths to the minimum (critical) soil depth required for landslide initiation in each hollow. Our data show that most hollow soil depths are close to their critical depth, with 62% of hollows having soils that are too thin to fail. Our results, supported by numerical modeling, reveal that landslide frequency in many humid landscapes may be insensitive to projected changes in the frequency of intense rainfall events.
Proteome Profiling of Urinary Exosomes Identifies Alpha 1-Antitrypsin and H2B1K as Diagnostic and Prognostic Biomarkers for Urothelial Carcinoma
Authors: Lin Shih-Yi , Chang Chao-Hsiang , Wu His-Chin , Lin Ching-Chan , Chang Kai-Po , Yang Chi-Rei , Huang Chi-Ping , Hsu Wu-Huei , Chang Chiz-Tzung , Chen Chao-Jung
Published: September 2016

MALDI-TOF spectrometry has not been used for urinary exosome analysis. We used it for determining UC biomarkers. From 2012 to 2015, we enrolled 129 consecutive patients with UC and 62 participants without UC. Exosomes from their urine were isolated, and analyzed through MALDI-TOF spectrometry. Immunohistochemical (IHC) analysis of another 122 UC and 26 non-UC tissues was conducted to verify the discovered biomarkers. Two peaks at m/z 5593 (fragmented peptide of alpha-1-antitrypsin; sensitivity, 50.4%; specificity, 96.9%) and m/z 5947 (fragmented peptide of histone H2B1K sensitivity, 62.0%; specificity, 92.3%) were identified as UC diagnosis exosome biomarkers. UC patients with detectable histone H2B1K showed 2.29- and 3.11-fold increased risks of recurrence and progression, respectively, compared with those with nondetectable histone H2B1K. Verification results of IHC staining revealed significantly higher expression of alpha 1-antitrypsin (p = 0.038) and H2B1K (p = 0.005) in UC tissues than in normal tissues. The expression of alpha 1-antitrypsin and H2B1K in UC tissues was significantly correlated with UC grades (p < 0.05). Urinary exosome proteins alpha 1-antitrypsin and histone H2B1K, which are identified through MALDI-TOF analysis, could facilitate rapid diagnosis and prognosis of UC.
Non-specific alarm calls trigger mobbing behavior in Hainan gibbons (Nomascus hainanus)
Authors: Deng Huaiqing , Gao Kai , Zhou Jiang
Published: September 2016

Alarm calls are important defensive behaviors. Here, we report the acoustic spectrum characteristics of alarm calls produced by Hainan gibbons (Nomascus hainanus) inhabiting Bawangling National Nature Reserve in Hainan, China. Analysis of call data collected from 2002–2014 shows that alarm calls are emitted by all family group members, except infants. Alarm behavior included simple short alarming calls (7–10 min) followed by longer variable-frequency mobbing calls lasting 5–12 min. The duration of individual alarming and mobbing calls was 0.078 ± 0.014 s and 0.154 ± 0.041 s at frequency ranges of 520–1000 Hz and 690–3920 Hz, respectively. Alarming call duration was positively associated with group size. The alarm calls can trigger mobbing behavior in Hainan gibbons; this is a defense way of social animals and first report among the primates’ species. The system of vocal alarm behavior described in this critically endangered species is simple and effective.
Bithionol blocks pathogenicity of bacterial toxins, ricin and Zika virus
Authors: Leonardi William , Zilbermintz Leeor , Cheng Luisa W. , Zozaya Josue , Tran Sharon H. , Elliott Jeffrey H. , Polukhina Kseniya , Manasherob Robert , Li Amy , Chi Xiaoli , Gharaibeh Dima , Kenny Tara , Zamani Rouzbeh , Soloveva Veronica , Haddow Andrew D. , Nasar Farooq , Bavari Sina , Bassik Michael C. , Cohen Stanley N. , Levitin Anastasia , Martchenko Mikhail
Published: September 2016

Diverse pathogenic agents often utilize overlapping host networks and hub proteins within these networks represent attractive targets for broad-spectrum drugs. Using bacterial toxins, we describe a new approach for discovering broad-spectrum therapies capable of inhibiting host proteins that mediate multiple pathogenic pathways. This approach can be widely used, as it combines genetic-based target identification with cell survival-based and protein function-based multiplex drug screens and concurrently discovers therapeutic compounds and their protein targets. Using B-lymphoblastoid cells derived from the HapMap Project cohort of persons of African, European and Asian ancestry we identified host caspases as hub proteins that mediate the lethality of multiple pathogenic agents. We discovered that an approved drug, Bithionol, inhibits host caspases and also reduces the detrimental effects of anthrax lethal toxin, diphtheria toxin, cholera toxin, Pseudomonas aeruginosa exotoxin A, Botulinum neurotoxin, ricin and Zika virus. Our study reveals the practicality of identifying host proteins that mediate multiple disease pathways and discovering broad-spectrum therapies that target these hub proteins.
SMC4, which is essentially involved in lung development, is associated with lung adenocarcinoma progression
Authors: Zhang Chengli , Kuang Manchao , Li Meng , Feng Lin , Zhang Kaitai , Cheng Shujun
Published: September 2016

Structural maintenance of chromosome 4 (SMC4) is a core subunit of condensin complexes that mainly contributes to chromosome condensation and segregation. Our previous study demonstrated that the gene expression profile during lung development is of great values for the study of lung cancer. In this study, we identified SMC4 through co-expression network analysis and clique percolation clustering using genes that constant changes during four stages of lung development. Gene ontology and KEGG pathway enrichment analysis demonstrated that SMC4 is closely related to cell cycle, cell adhesion and RNA processing in lung development and carcinogenesis. Moreover, SMC4 is overexpressed in lung adenocarcinoma tissues and acts as an independent prognostic factor. SMC4 knockdown significantly inhibits the proliferation and invasion of A549 cells. Furthermore, we found that SMC4 interacts with DDX46 (DEAD-box helicase 46). In conclusion, the pivotal role of SMC4 in lung development and carcinogenesis suggests that genes with a similar expression pattern to SMC4 in lung development may also contribute to lung cancer progression. The identification of genes that are essentially involved in development through a comparative study between development and cancer may be a practical strategy for discovering potential biomarkers and illuminating the mechanisms of carcinogenesis.
Optimization of Treatment Geometry to Reduce Normal Brain Dose in Radiosurgery of Multiple Brain Metastases with Single–Isocenter Volumetric Modulated Arc Therapy
Authors: Wu Qixue , Snyder Karen Chin , Liu Chang , Huang Yimei , Zhao Bo , Chetty Indrin J. , Wen Ning
Published: September 2016

Treatment of patients with multiple brain metastases using a single-isocenter volumetric modulated arc therapy (VMAT) has been shown to decrease treatment time with the tradeoff of larger low dose to the normal brain tissue. We have developed an efficient Projection Summing Optimization Algorithm to optimize the treatment geometry in order to reduce dose to normal brain tissue for radiosurgery of multiple metastases with single-isocenter VMAT. The algorithm: (a) measures coordinates of outer boundary points of each lesion to be treated using the Eclipse Scripting Application Programming Interface, (b) determines the rotations of couch, collimator and gantry using three matrices about the cardinal axes, (c) projects the outer boundary points of the lesion on to Beam Eye View projection plane, (d) optimizes couch and collimator angles by selecting the least total unblocked area for each specific treatment arc and (e) generates a treatment plan with the optimized angles. The results showed significant reduction in the mean dose and low dose volume to normal brain, while maintaining the similar treatment plan qualities on the thirteen patients treated previously. The algorithm has the flexibility with regard to the beam arrangements and can be integrated in the treatment planning system for clinical application directly.
Gamma-H2AX upregulation caused by Wip1 deficiency increases depression-related cellular senescence in hippocampus
Authors: He Zhi-Yong , Wang Wen-Yue , Hu Wei-Yan , Yang Lu , Li Yan , Zhang Wei-Yuan , Yang Ya-Shu , Liu Si-Cheng , Zhang Feng-Lan , Mei Rong , Xing Da , Xiao Zhi-Cheng , Zhang Ming
Published: September 2016

The PP2C family member Wild-type p53-induced phosphatase 1 (Wip1) critically regulates DNA damage response (DDR) under stressful situations. In the present study, we investigated whether Wip1 expression was involved in the regulation of DDR-induced and depression-related cellular senescence in mouse hippocampus. We found that Wip1 gene knockout (KO) mice showed aberrant elevation of hippocampal cellular senescence and of γ-H2AX activity, which is known as a biomarker of DDR and cellular senescence, indicating that the lack of Wip1-mediated γ-H2AX dephosphorylation facilitates cellular senescence in hippocampus. Administration of the antidepressant fluoxetine had no significant effects on the increased depression-like behaviors, enriched cellular senescence and aberrantly upregulated hippocampal γ-H2AX activity in Wip1 KO mice. After wildtype C57BL/6 mice were exposed to the procedure of chronic unpredictable mild stress (CUMS), cellular senescence and γ-H2AX activity in hippocampus were also elevated, accompanied by the suppression of Wip1 expression in hippocampus when compared to the control group without CUMS experience. These CUMS-induced symptoms were effectively prevented following fluoxetine administration in wildtype C57BL/6 mice, with the normalization of depression-like behaviors. Our data demonstrate that Wip1-mediated γ-H2AX dephosphorylation may play an important role in the occurrence of depression-related cellular senescence.
Differential roles of NF-Y transcription factor in ER chaperone expression and neuronal maintenance in the CNS
Authors: Yamanaka Tomoyuki , Tosaki Asako , Miyazaki Haruko , Kurosawa Masaru , Koike Masato , Uchiyama Yasuo , Maity Sankar N. , Misawa Hidemi , Takahashi Ryosuke , Shimogori Tomomi , Hattori Nobutaka , Nukina Nobuyuki
Published: September 2016

The mammalian central nervous system (CNS) contains various types of neurons with different neuronal functions. In contrast to established roles of cell type-specific transcription factors on neuronal specification and maintenance, whether ubiquitous transcription factors have conserved or differential neuronal function remains uncertain. Here, we revealed that inactivation of a ubiquitous factor NF-Y in different sets of neurons resulted in cell type-specific neuropathologies and gene downregulation in mouse CNS. In striatal and cerebellar neurons, NF-Y inactivation led to ubiquitin/p62 pathologies with downregulation of an endoplasmic reticulum (ER) chaperone Grp94, as we previously observed by NF-Y deletion in cortical neurons. In contrast, NF-Y inactivation in motor neurons induced neuronal loss without obvious protein deposition. Detailed analysis clarified downregulation of another ER chaperone Grp78 in addition to Grp94 in motor neurons and knockdown of both ER chaperones in motor neurons recapitulated the pathology observed after NF-Y inactivation. Finally, additional downregulation of Grp78 in striatal neurons suppressed ubiquitin accumulation induced by NF-Y inactivation, implying that selective ER chaperone downregulation mediates different neuropathologies. Our data suggest distinct roles of NF-Y in protein homeostasis and neuronal maintenance in the CNS by differential regulation of ER chaperone expression.
A general solution for opening double-stranded DNA for isothermal amplification
Authors: Chen Gangyi , Dong Juan , Yuan Yi , Li Na , Huang Xin , Cui Xin , Tang Zhuo
Published: September 2016

Nucleic acid amplification is the core technology of molecular biology and genetic
engineering. Various isothermal amplification techniques have been developed as
alternatives to polymerase chain reaction (PCR). However, most of these
methods can only detect single stranded nucleic acid. Herein, we put forward a
simple solution for opening double-stranded DNA for isothermal detection methods.
The strategy employs recombination protein from E. coli (RecA) to form
nucleoprotein complex with single-stranded DNA, which could scan double-stranded
template for homologous sites. Then, the nucleoprotein can invade the
double-stranded template to form heteroduplex in the presence of ATP, resulting in
the strand exchange. The ATP regeneration system could be eliminated by using high
concentration of ATP, and the 3′-OH terminal of the invasion strand can
be recognized by other DNA modifying enzymes such as DNA polymerase or DNA ligase.
Moreover, dATP was found to be a better cofactor for RecA, which make the
system more compatible to DNA polymerase. The method described here is a general
solution to open dsDNA, serving as a platform to develop more isothermal nucleic
acids detection methods for real DNA samples based on it.
On-chip fluorescent labeling using reversed-phase monoliths and microchip electrophoretic separations of selected preterm birth biomarkers
Authors: Sonker Mukul , Yang Rui , Sahore Vishal , Kumar Suresh , Woolley Adam T.
Published: September 2016

On-chip preconcentration, purification, and fluorescent labeling are desirable sample preparation steps to achieve complete automation in integrated microfluidic systems.
Species identification of ancient leather objects by the use of the enzyme-linked immunosorbent assay
Authors: Liu Yi , Li Yi , Chang Runxing , Zheng Hailing , Zhou Yang , Li Menglu , Hu Zhiwen , Wang Bing
Published: September 2016

A novel immunological method for the species identification of ancient leather.
Novel synthesis of chitosan protected platinum nanoparticles based on gas–liquid interfacial reactions and their application for electrochemical sensing of hydrogen peroxide
Authors: Liu Jianbo , Bai Wushuang , Zhang Juncai , Zheng Jianbin
Published: September 2016

A gas–liquid reaction was proposed for the controllable synthesis of Pt nanoparticles, which exhibited uniform morphology without any aggregation.
Augmentation of productivity in olefin cross-metathesis: maleic acid does the trick!
Authors: Ferreira Leonildo A. , Schrekker Henri S.
Published: September 2016

Why use the protected esters when the free acids result in better catalytic performances?
Novel aminoalkyl tris-cyclometalated iridium complexes as cellular stains
Authors: Sansee A. , Meksawangwong S. , Chainok K. , Franz K. J. , Gál M. , Pålsson L.-O. , Puniyan W. , Traiphol R. , Pal R. , Kielar F.
Published: September 2016

Novel tris-cyclometalated luminescent iridium complexes capable of staining cells and showing in cellulo lifetimes in the microsecond regime are reported.
Multiplex cell microarrays for high-throughput screening
Authors: Berthuy Ophélie I. , Muldur Sinan K. , Rossi François , Colpo Pascal , Blum Loïc J. , Marquette Christophe A.
Published: September 2016

Microarray technology was developed in the early 1990s and transferred lately to the development of cell microarrays.
Zinc complexes formed by 2,2′-bipyridine and 1,10-phenanthroline moieties combined with 2-azanorbornane: modular chiral catalysts for aldol reactions
Authors: Wojaczyńska Elżbieta , Skarżewski Jacek , Sidorowicz Łukasz , Wieczorek Robert , Wojaczyński Jacek
Published: September 2016

Zinc complexes of new hybrid chiral imine ligands based on a bicyclic skeleton appear to be effective modular catalysts in asymmetric aldol reactions.
Multiple stimuli-responsive supramolecular gels constructed from metal–organic cycles
Authors: Li Lijie , Cong Yong , He Lipeng , Wang Yongyue , Wang Jun , Zhang Fu-Ming , Bu Weifeng
Published: September 2016

Two supramolecular networks are constructed from a crown ether based metal–organic cycle and dibenzylammonium based poly(ε-caprolactone)s through multiple host–guest interactions. One of the networks can form organogels at higher concentrations, which show multiple stimuli-responsive behaviors.
LiAlH4supported on TiO2/hierarchically porous carbon nanocomposites with enhanced hydrogen storage properties
Authors: Zhao Yaran , Han Mo , Wang Haixia , Chen Chengcheng , Chen Jun
Published: September 2016

LiAlH4supported on TiO2/hierarchically porous carbon (LAH–TiO2/HPC) nanocomposites were prepared and they exhibited enhanced hydrogen storage performance.
Kinetic study on low temperature coalescence of carboxylate-protected Ag nanoparticles for interconnect applications
Authors: Song Jenn-Ming , Pai Tsung-Yun , Hsieh Kun-Hung , Lai Ming-Yan , Cheng Chi-Nan , Liang Sin-Yong , Lee Hsin-Yi , Chen Lung-Tai
Published: September 2016

Coalescence of carboxylate-capped Ag nanoparticles can be achieved by soaking the deposits in ascorbic acid solution. Long-chain carboxylates are easier to remove. Conductive and bendable films can form on PDMS substrate using this method.
A phenanthroline-derived ligand and its complexation with Pd(ii): from ligand design, synthesis and Pd(ii) complexes structures to its application
Authors: Xu Lei , Zhang Anyun , Lu Yanchao , Yang Hua , Liu Ziyang
Published: September 2016

This paper reports the first example of a phenanthroline-derived bis-opened-triazine ligand showing high selectivity and fast extraction rate toward Pd(ii).
Facile fabrication of metal-free urchin-like g-C3N4 with superior photocatalytic activity
Authors: Luo Lei , Zhang Anfeng , Janik Michael J. , Song Chunshan , Guo Xinwen
Published: September 2016

Spherical urchin-like graphitic carbon nitride nanoparticles were fabricated and exhibited almost 12 times higher activity during RhB photodegradation.
Continuously tunable emission color based on the molecular aggregation of (2Z,2′Z)-2,2′-(1,4-phenylenae)bis(3-(4-(dodecyloxy)phenyl)acrylonitrile)
Authors: Lu Hongbo , Zhang Chao , Xia Guo , Wu Shaojun , Zhang Guobing , Yang Jiaxiang , Qiu Longzhen
Published: September 2016

A luminescent liquid crystal self-assembles to a layer structure or a helical structure with different pitch length depending on the stacking rate; a photoluminescence spectrum blue-shift from 600 nm to 506 nm.
Correction: Rhus verniciflua as a green corrosion inhibitor for mild steel in 1 M H2SO4
Authors: Prabakaran Mayakrishnan , Kim Seung-Hyun , Hemapriya Venkatesan , Gopiraman Mayakrishnan , Kim Ick Soo , Chung Ill-Min
Published: September 2016

Correction for ‘Rhus verniciflua as a green corrosion inhibitor for mild steel in 1 M H2SO4’ by Mayakrishnan Prabakaran et al., RSC Adv., 2016, 6, 57144–57153.