bluuebunny/crossref_metadata_2025 huggingface dataset:
Studies in vitro on infectivity and sensitivity to antileishmanial drugs in New World Leishmania species transfected with the green fluorescent protein [pIR3(-)-eGFP]
Authors: PALACIOS GENESIS , PARODI ADRIANA , UPEGUI YULIETH A. , MONTOYA ANDRES , PULIDO SERGIO , VÉLEZ IVÁN D. , ROBLEDO SARA M.
Published: August 2017

Current chemotherapeutic agents for leishmaniasis have several disadvantages interfering with the effective treatment and therefore more and better antileishmanial drugs are needed. Discovery of candidates for leishmaniasis treatment requires not only accurate and precise methodologies but also well-known biological system to measure infectivity of parasites and antileishmanial activity of the new compounds. Significant variation in the in vitro and in vivo infectivity and sensitivity to established and experimental drugs in Leishmania strains are reported. This work reports the in vitro biological behavior and antileishmanial drugs sensitivity of different green fluorescent protein transfectant Leishmanias strains. The in vitro growth kinetic and infectivity to U937 cells vary slightly in the Leishmania transfectant strains in comparison with their correspondant wild-type. However, the insertion of the pIR3(-)-eGFP may affect the sensitivity of the parasites to meglumine antimoniate (MA) and miltefosine but not to amphotericin B (AMB) and pentamidine isethionate. In consequence, AMB or pentamidine isethionate but not MA or miltefosine should be used as antileishmanial control drugs during in vitro assays of antileishmanial activity. Furthermore, is recommended to test compounds against more than one Leishmania strain in order to verify that the antileihmanial activity of these compound is similar among species.
Stage-dependent behavioural changes but early castration induced by the acanthocephalan parasitePolymorphus minutusin itsGammarus pulexintermediate host
Authors: BAILLY YANN , CÉZILLY FRANK , RIGAUD THIERRY
Published: August 2017

Multidimensionality in parasite-induced phenotypic alterations (PIPA) has been observed in a large number of host–parasite associations, particularly in parasites with complex life cycles. However, it is still unclear whether such a syndrome is due to the successive activation of independent PIPAs, or results from the synchronous disruption of a single mechanism. The aim of the present study was to investigate the onset and progression of two PIPAs (a behavioural alteration: reversion of geotaxis, and castration) occurring in the crustacean amphipodGammarus pulexinfected with the acanthocephalanPolymorphus minutus, at different parasite developmental stages. Modifications of geotaxis in hosts differed according to the parasite developmental stage. Whereas the cystacanth stage induced a negative geotaxis (exposing the gammarid to predation by birds, the definitive hosts), the acanthella stage, not yet infective for the definitive host, induced a stronger positive geotaxis (presumably protecting gammarids from bird predation). In contrast, castration was almost total at the acanthella stage, with no significant variation in the intensity according to parasite maturation. Finally, no significant correlation was found between the intensity of behavioural changes and the intensity of castration. We discuss our results in relation with current views on the evolution of multidimensionality in PIPA.
Parasitic nematodes of the genusSyphaciaSeurat, 1916 infecting Muridae in the British Isles, and the peculiar case ofSyphacia frederici
Authors: STEWART ALEX , LOWE ANN , SMALES LESLEY , BAJER ANNA , BRADLEY JAN , DWUŻNIK DOROTA , FRANSSEN FRITS , GRIFFITH JACK , STUART PETER , TURNER CYAN , ZALEŚNY GRZEGORZ , BEHNKE JERZY M.
Published: August 2017

Syphacia stroma(von Linstow, 1884) Morgan, 1932 andSyphacia fredericiRoman, 1945 are oxyurid nematodes that parasitize two murid rodents,Apodemus sylvaticusandApodemus flavicollis,on the European mainland. OnlyS. stromahas been recorded previously inApodemusspp. from the British Isles. Despite the paucity of earlier reports, we identifiedS. fredericiin four disparate British sites, two in Nottinghamshire, one each in Berkshire and Anglesey, Wales. Identification was based on their site in the host (caecum and not small intestine), on key morphological criteria that differentiate this species fromS. stroma(in particular the tail of female worms) and by sequencing two genetic loci (cytochrome C oxidase 1 gene and a section of ribosomal DNA). Sequences derived from both genetic loci of putative BritishS. fredericiisolates formed a tight clade with sequences from continental worms known to beS. frederici, clearly distinguishing these isolates fromS. stromawhich formed a tight clade of its own, distinct from clades representative ofSyphacia obvelatafromMusandS. murisfromRattus. The data in this paper therefore constitute the first record ofS. fredericifrom British wood mice, and confirm the status of this species as distinct from bothS. obvelataandS. stroma.
The nature and efficacy of culturally-adapted psychosocial interventions for schizophrenia: a systematic review and meta-analysis
Authors: Degnan A. , Baker S. , Edge D. , Nottidge W. , Noke M. , Press C. J. , Husain N. , Rathod S. , Drake R. J.
Published: August 2017

Background

Evidence-based psychosocial treatments for schizophrenia founded on Western belief systems and values may not be efficacious in different cultures without adaptation. This systematic review analyses the nature and outcomes of culturally-adapted psychosocial interventions in schizophrenia, examining how interventions have been adapted, their efficacy and what features drive heterogeneity in outcome.

Method

Articles identified by searching electronic databases from inception to 3 March 2016, reference lists and previous reviews were independently screened by two authors for eligible controlled trials. Data on the nature of adaptations was analysed inductively using thematic analyses. Meta-analyses were conducted using random effects models to calculate effect sizes (Hedges’ g) for symptoms.

Results

Forty-six studies with 7828 participants were included, seven adapted for minority populations. Cultural adaptations were grouped into nine themes: language, concepts and illness models, family, communication, content, cultural norms and practices, context and delivery, therapeutic alliance, and treatment goals. Meta-analyses showed significant post-treatment effects in favour of adapted interventions for total symptom severity (n = 2345, g: −0.23, 95% confidence interval (CI) −0.36 to −0.09), positive (n = 1152, g: −0.56, 95% CI −0.86 to −0.26), negative (n = 855, g: −0.39, 95% CI −0.63 to −0.15), and general (n = 525, g: −0.75, CI −1.21 to −0.29) symptoms.

Conclusions

The adaptation process can be described within a framework that serves as a benchmark for development or assessment of future adaptations. Culturally adapted interventions were more efficacious than usual treatment in proportion to the degree of adaptation. There is insufficient evidence to show that adapted interventions are better than non-adapted interventions. Features of context, intervention and design influenced efficacy. Investigating whether adaptation improves efficacy, most importantly amongst ethnic minorities, requires better designed trials with comparisons against unadapted interventions.
Why the West Became Wild
Authors: Larson Jennifer M.
Published: August 2017

Settlers flocking to boomtowns on the American western frontier were faced with the same task that communities in weak states across the globe face in contemporary times: self-governance. Peer sanctions can enforce cooperation in these environments, but their efficacy depends on the social networks that transmit information from peer to peer. The author uses a game-theoretic model to show that peripheral network positions can generate such strong incentives to misbehave that persistent cheating occurs in equilibrium. The model reveals that groups maintaining high levels of cooperation that face shocks to their strategic environment or to their network can ratchet down into less cooperative equilibria in which the most peripheral become ostracized. Furthermore, population change that features rapid growth, high turnover, and enclave settlements can undermine cooperation. The insights from this article help to explain the trajectory of cooperation in the mining towns of the Wild West in which high levels of cooperation deteriorated as the population surged, and help to make sense of why only certain nonwhite settlers were targets of hostility and racism.
Robot-to-human feedback and automatic object grasping using an RGB-D camera–projector system
Authors: Shen Jinglin , Gans Nicholas
Published: August 2017

This paper presents a novel system for human–robot interaction in object-grasping applications. Consisting of an RGB-D camera, a projector and a robot manipulator, the proposed system provides intuitive information to the human by analyzing the scene, detecting graspable objects and directly projecting numbers or symbols in front of objects. Objects are detected using a visual attention model that incorporates color, shape and depth information. The positions and orientations of the projected numbers are based on the shapes, positions and orientations of the corresponding objects. Users select a grasping target by indicating the corresponding number. Projected arrows are then created on the fly to guide a robotic arm to grasp the selected object using visual servoing and deliver the object to the human user. Experimental results are presented to demonstrate how the system is used in robot grasping tasks.
Research on Ship Classification Based on Trajectory Features
Authors: Sheng Kai , Liu Zhong , Zhou Dechao , He Ailin , Feng Chengxu
Published: August 2017

It is important for maritime authorities to effectively classify and identify unknown types of ships in historical trajectory data. This paper uses a logistic regression model to construct a ship classifier by utilising the features extracted from ship trajectories. First of all, three basic movement patterns are proposed according to ship sailing characteristics, with related sub-trajectory partitioning algorithms. Subsequently, three categories of trajectory features with their extraction methods are presented. Finally, a case study on building a model for classifying fishing boats and cargo ships based on real Automatic Identification System (AIS) data is given. Experimental results indicate that the proposed classification method can meet the needs of recognising uncertain types of targets in historical trajectory data, laying a foundation for further research on camouflaged ship identification, behaviour pattern mining, outlier behaviour detection and other applications.
Role of Demographic and Clinical Factors in Cognitive Functioning of Persons with Relapsing-Remitting and Progressive Multiple Sclerosis
Authors: Costa Silvana L. , DeLuca John , Sandroff Brian M. , Goverover Yael , Chiaravalloti Nancy D.
Published: August 2017

Background: Age and time post-diagnosis can significantly impact cognitive and motor functions in multiple sclerosis (MS); however, studies often fail to account for these factors when assessing differences between disease courses. Objectives: Examine differences between relapsing-remitting and progressive MS in cognition, motor function, and everyday activities, controlling for age, education, and time post-diagnosis. Methods: Twenty-one persons with relapsing-remitting MS (RRMS group), 21 with progressive MS (PMS group), and 21 healthy participants (HCs), matched on age, education, and time post-diagnosis, completed tests of cognitive abilities, motor functions, and everyday functional activities. Results: The two groups with MS did not differ on cognitive performance. Poorer performance in processing speed was noted in both MS groups in comparison with the HC group. Motor function was worse for the PMS group compared with the HC and RRMS groups. The RRMS group showed poorer upper limb functioning compared to the HC group. The PMS group had more difficulty with everyday activities as compared with both the RRMS and HC group. Conclusions: When comparing differences in functioning between MS disease courses, attention should be paid to the demographic characteristics of the samples. (JINS, 2018, 24, 139–146)
The Last Days of the Song Dynasty: Evidence of the Flight of Song Officials to Southeast Asia before the Mongol Invasions
Authors: KESSLER ADAM T.
Published: August 2017

In the first part of the 13th century ce, Khubilai Khan's armies began their invasion of the Southern Song dynasty (1127-1279). When they reached the Song capital Lin'anfu at Hangzhou City, Zhejiang province, at the beginning of 1276, the Song officials decided to flee south with the two Song child heirs to the throne. This article examines ancient records of the flight of the Song court with particular emphasis on the history of its famous Prime Minister Chen Yizhong. Archaeological evidence is further evaluated as it relates to Chen's exploits within China and in Southeast Asia.
Characterisation of small photon field outputs in a heterogeneous medium using X-ray voxel Monte Carlo dose calculation algorithm
Authors: Nithiyanantham Karthikeyan , Mani Ganesh K. , Raju Sambasivaselli , Velliangiri Senniandavar , Paramasivam Maniyan , Palaniappan Karrthick K. , Jain Sandeep
Published: August 2017

Aim

To characterise small photon beams using the Monte Carlo dose calculation algorithm for small field ranges in a heterogeneous medium.

Materials and method

An in-house phantom constructed with three different mediums, foam, polymethyl methacrylate and delrin resembling the densities of lung, soft tissue and bone respectively, was used in this study. Photon beam energies of 6 and 15 MV and field sizes of 8×8, 16×16, 24×24, 32×32 and 40×40 mm using X-ray voxel Monte Carlo (XVMC) algorithm using different detectors were validated. The relative output factor was measured in three different mediums having six different tissue interfaces; at the depth of 0, 1, 2 and 3 cm. The planar dose verification was undertaken using gafchromic films and considered dose at the lung and bone medium interfaces. For all the measurements, 104×104 mm was taken as the reference field size. The relative output factor for all other field sizes was taken and compared with planning system calculated values.

Results

From field size 16×16 mm and above, the relative output factors were analysed in bone and soft tissue medium having lung as first medium. The maximum deviations were observed as 1·8 and 1·3% for 6 MV and 2·5 and 1·1% for 15 MV photon beams for bone and soft tissue, respectively. For lung as measurement medium, the maximum deviation of 14·8 and 19·2% were observed and having bone as first medium with 8×8 mm for 6 and 15 MV photon beams, respectively. The fluence verification of dose spectrum for the lung–bone interface scenarios with smaller field sizes were found within 2% of deviation with treatment planning system (TPS).

Conclusion

The accuracy of dose calculations for small field sizes in XVMC-based treatment planning algorithm was studied in different inhomogeneous mediums. It was found that the results correlated with measurement data for field size 16×16 mm and above. Noticeable deviation was observed for the smallest field size of 8×8 mm with interfaces of significant change in density. The observed results demands further analysis of work with smaller field sizes.
Improving adherence to heart failure management guidelines via abductive reasoning
Authors: CHEN ZHUO , SALAZAR ELMER , MARPLE KYLE , GUPTA GOPAL , TAMIL LAKSHMAN , CHEERAN DANIEL , DAS SANDEEP , AMIN ALPESH
Published: August 2017

Management of chronic diseases, such as heart failure, is a major public health problem. A standard approach to managing chronic diseases by medical community is to have a committee of experts develop guidelines that all physicians should follow. Due to their complexity, these guidelines are difficult to implement and are adopted slowly by the medical community at large. We have developed a physician advisory system that codes the entire set of clinical practice guidelines for managing heart failure using answer set programming. In this paper, we show how abductive reasoning can be deployed to find missing symptoms and conditions that the patient must exhibit in order for a treatment prescribed by a physician to work effectively. Thus, if a physician does not make an appropriate recommendation or makes a non-adherent recommendation, our system will advise the physician about symptoms and conditions that must be in effect for that recommendation to apply. It is under consideration for acceptance in TPLP.
Logic programming approaches for routing fault-free and maximally parallel wavelength-routed optical networks-on-chip (Application paper)
Authors: GAVANELLI MARCO , NONATO MADDALENA , PEANO ANDREA , BERTOZZI DAVIDE
Published: August 2017

One promising trend in digital system integration consists of boosting on-chip communication performance by means of silicon photonics, thus materializing the so-called Optical Networks-on-Chip. Among them, wavelength routing can be used to route a signal to destination by univocally associating a routing path to the wavelength of the optical carrier. Such wavelengths should be chosen so to minimize interferences among optical channels and to avoid routing faults. As a result, physical parameter selection of such networks requires the solution of complex constrained optimization problems. In previous work, published in the proceedings of the International Conference on Computer-Aided Design, we proposed and solved the problem of computing the maximum parallelism obtainable in the communication between any two endpoints while avoiding misrouting of optical signals. The underlying technology, only quickly mentioned in that paper, is Answer Set Programming. In this work, we detail the Answer Set Programming approach we used to solve such problem.

Another important design issue is to select the wavelengths of optical carriers such that they are spread across the available spectrum, in order to reduce the likelihood that, due to imperfections in the manufacturing process, unintended routing faults arise. We show how to address such problem in Constraint Logic Programming on Finite Domains.
Inclusive gender: Why tackling gender hierarchies cannot be at the expense of human rights and the humanitarian imperative
Authors: Dolan Chris
Published: August 2017

The “Debate” section of the Review aims to contribute to the reflection on current ethical, legal or operational controversies around humanitarian issues. In its issue on “Sexual Violence in Armed Conflict” (Vol. 96, No. 894, 2014), the Review published an Opinion Note by Chris Dolan entitled “Letting Go of the Gender Binary: Charting New Pathways for Humanitarian Interventions on Gender-Based Violence”, arguing for a shift in the conceptualization of gender-based violence (GBV) in humanitarian settings from an emphasis on gender equality to an ethos of gender inclusivity. Jeanne Ward's reply, “It's Not About the Gender Binary, It's About the Gender Hierarchy”, was published in a later issue of the Review (Vol. 98, No. 901, 2016). Ward suggested retaining a focus on women and girls in GBV work, while moving forward in partnership with those who wish to accelerate programming directed towards men and lesbian, gay, bisexual, transgender and intersex (LGBTI) communities broadly. In this issue, Dolan responds to Ward's position, pointing to empirical and practical developments that have advanced the understanding of how to effectively respond to GBV, including GBV perpetrated against men, boys and members of the LGBTI community. Dolan calls for the IASC Guidelines to be revised in 2020 to be the guiding text on preventing and responding to GBV in humanitarian settings, and explores what it means to do inclusive gender while also tackling hierarchies.
Protecting the Credit of the State - Speculation, Trust, and Sovereignty in Interwar France
Authors: Delalande Nicolas
Published: August 2017

This article investigates the creation, in 1924, of a new offence in French law, aimed at punishing anyone found guilty of “breaching the credit of the state”—that is, of discourses or practices likely to damage the financial reputation of the French state. In the midst of a destabilizing budgetary and monetary crisis, surrounded by fierce political disputes, “the credit of the state” was legally defined as an essential attribute of sovereignty, to be defended against internal and external threats. However, the intellectual history of public credit and the analysis of archival material relating to this new offence show how difficult it was for courts to draw a line between the freedom of the market and the protection of public order. More broadly, this research emphasizes the interconnected role of material and immaterial elements in promoting public trust in the value of the papers (bonds and currency) issued by the state.
Rolle von Ernährung und Lebensstil für die Verhütung und Therapien von Fettstoffwechselstörungen
Authors: Suter Paolo M.
Published: August 2017

Zusammenfassung. Trotz aller Kontroversen ist die Empfehlung der Kontrolle der Zufuhr an gesättigten Fetten und Cholesterin bei gleichzeitiger Optimierung der Zufuhr an einfach- und mehrfach ungesättigten Fetten immer noch gültig, sollte aber nicht unabhängig von anderen beeinflussbaren Determinanten betrachtet werden. Diese Empfehlungen können am einfachsten durch Beachtung des gesamten Essmusters erreicht werden, das eigentlich einem semi-vegetarischen Essmuster mit geringer Energiedichte entspricht. Es gilt, regelmässig alle Komponenten des «Foodoms» mit der Ernährung aufzunehmen.
Hypertriglyzeridämie und HDL-Mangel
Authors: von Eckardstein Arnold
Published: August 2017

Zusammenfassung. Mit steigenden Plasma-Konzentrationen der Triglyzeride nehmen die Risiken für atherosklerotische Herz-Kreislauf-Erkrankungen (ASKVK) und akute Pankreatitis zu. Ein niedriger HDL-Cholesterin-Spiegel erhöht das ASKVK-Risiko. Bei hohen Konzentrationen von HDL-Cholesterin ist das Risiko für ASKVK nicht vermindert, aber das für Mortalität erhöht. Hypertriglyzeridämie und niedriges HDL-Cholesterin treten häufig gemeinsam und zusammen mit anderen Risikofaktoren auf. Genetische Studien und gescheiterte Interventionsstudien machen eine kausale Beziehung zwischen HDL-Cholesterin und ASKVK unwahrscheinlich, sodass die Erhöhung des HDL-Cholesterin-Spiegels kein Behandlungsziel ist. Genetische Analysen sprechen zwar für eine kausale Beziehung der triglyzeridreichen Lipoproteine zum kardiovaskulären Risiko, aber es gibt keine Erfolgsnachweise aus Interventionsstudien. Deswegen ist die Senkung der Triglyzeride nur bei Chylomikronämie primäres Behandlungsziel. Bei moderater Hypertriglyzeridämie (<10 mmol/l) und niedrigem HDL-Cholesterin ist die Kontrolle anderer ASKVK-Risikofaktoren, insbesondere die Erreichung des LDL-Cholesterin-Zielwertes, primäres Behandlungsziel. Hohe Triglyzerid-Konzentrationen lassen sich besonders gut durch Lebensstil (körperliche Aktivität), Ernährungsweise (Vermeidung von Alkohol, gesättigten Fettsäuren und leicht resorbierbaren Kohlenhydraten) und Behandlung der Grundkrankheit (vor allem Diabetes) senken. Fibrate und Omega-3-Fettsäuren kommen in Betracht, wenn diese Massnahmen versagen.
Lipoprotein(a) – es wird Zeit, das Dornröschen wach zu küssen
Authors: Kronenberg Florian
Published: August 2017

Zusammenfassung. Hohe Lp(a)-Konzentrationen sind mit koronarer Herzkrankheit (KHK) und Aortenstenosen assoziiert. Dieser Zusammenhang ist mit hoher Wahrscheinlichkeit kausal und wurde durch genetische und epidemiologische Studien und zum Teil auch interventionelle Daten sehr eindrücklich untermauert. Die therapeutischen Möglichkeiten sind zwar bis auf Ausnahmen momentan noch beschränkt, es gibt aber begründete Hoffnung für die nächsten Jahre. Das Wissen, dass sich hinter einer KHK nicht selten ein erhöhter Lp(a)-Spiegel versteckt, ist zurzeit leider noch zu wenig im klinischen Alltag angekommen. Das «Dornröschen» Lp(a) muss für die klinische Diagnostik dringend wachgeküsst werden. Bei Feststellung hoher Konzentrationen sind ein strenges Management anderer Risikofaktoren und die Beobachtung des Patienten gefordert. Dies schliesst auch die Beratung und Beobachtung eventueller direkter Familienangehöriger mit ein. Damit kann oft die für die Patienten quälende Frage nach dem «Warum» beantwortet und unnötiges weiteres Leid vermieden werden.
Howling at the Moon with Eclipse Enthusiasts
Authors: Kumar Mohi
Published: August 2017

From the reporters who stared at goats to poets who tweeted haiku, eclipse watchers across the nation flaunted their weird.
Correction: Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail
Authors: Adema Coen M. , Hillier LaDeana W. , Jones Catherine S. , Loker Eric S. , Knight Matty , Minx Patrick , Oliveira Guilherme , Raghavan Nithya , Shedlock Andrew , do Amaral Laurence Rodrigues , Arican-Goktas Halime D. , Assis Juliana G. , Baba Elio Hideo , Baron Olga L. , Bayne Christopher J. , Bickham-Wright Utibe , Biggar Kyle K. , Blouin Michael , Bonning Bryony C. , Botka Chris , Bridger Joanna M. , Buckley Katherine M. , Buddenborg Sarah K. , Lima Caldeira Roberta , Carleton Julia , Carvalho Omar S. , Castillo Maria G. , Chalmers Iain W. , Christensens Mikkel , Clifton Sandra , Cosseau Celine , Coustau Christine , Cripps Richard M. , Cuesta-Astroz Yesid , Cummins Scott F. , Di Stefano Leon , Dinguirard Nathalie , Duval David , Emrich Scott , Feschotte Cédric , Feyereisen Rene , FitzGerald Peter , Fronick Catrina , Fulton Lucinda , Galinier Richard , Gava Sandra G. , Geusz Michael , Geyer Kathrin K. , Giraldo-Calderón Gloria I. , de Souza Gomes Matheus , Gordy Michelle A. , Gourbal Benjamin , Grunau Christoph , Hanington Patrick C. , Hoffmann Karl F. , Hughes Daniel , Humphries Judith , Jackson Daniel J. , Jannotti-Passos Liana K. , de Jesus Jeremias Wander , Jobling Susan , Kamel Bishoy , Kapusta Aurélie , Kaur Satwant , Koene Joris M. , Kohn Andrea B. , Lawson Dan , Lawton Scott P. , Liang Di , Limpanont Yanin , Liu Sijun , Lockyer Anne E. , Lovato Ty Anna L. , Ludolf Fernanda , Magrini Vince , McManus Donald P. , Medina Monica , Misra Milind , Mitta Guillaume , Mkoji Gerald M. , Montague Michael J. , Montelongo Cesar , Moroz Leonid L. , Munoz-Torres Monica C. , Niazi Umar , Noble Leslie R. , Oliveira Francislon S. , Pais Fabiano S. , Papenfuss Anthony T. , Peace Rob , Pena Janeth J. , Pila Emmanuel A. , Quelais Titouan , Raney Brian J. , Rast Jonathan P. , Rollinson David , Rosse Izinara C. , Rotgans Bronwyn , Routledge Edwin J. , Ryan Kathryn M. , Scholte Larissa L. S. , Storey Kenneth B. , Swain Martin , Tennessen Jacob A. , Tomlinson Chad , Trujillo Damian L. , Volpi Emanuela V. , Walker Anthony J. , Wang Tianfang , Wannaporn Ittiprasert , Warren Wesley C. , Wu Xiao-Jun , Yoshino Timothy P. , Yusuf Mohammed , Zhang Si-Ming , Zhao Min , Wilson Richard K.
Published: August 2017

Nature Communications 8: Article number: 15451 (2017); Published 16 May 2017; Updated 23 August 2017 The original version of this Article contained an error in the spelling of the author Leon Di Stefano, which was incorrectly given as Leon di Stephano. This has now been corrected in both the PDF andHTML versions of the Article.
Poliovirus intrahost evolution is required to overcome tissue-specific innate immune responses
Authors: Xiao Yinghong , Dolan Patrick Timothy , Goldstein Elizabeth Faul , Li Min , Farkov Mikhail , Brodsky Leonid , Andino Raul
Published: August 2017

RNA viruses, such as poliovirus, have a great evolutionary capacity, allowing them to quickly adapt and overcome challenges encountered during infection. Here we show that poliovirus infection in immune-competent mice requires adaptation to tissue-specific innate immune microenvironments. The ability of the virus to establish robust infection and virulence correlates with its evolutionary capacity. We further identify a region in the multi-functional poliovirus protein 2B as a hotspot for the accumulation of minor alleles that facilitate a more effective suppression of the interferon response. We propose that population genetic dynamics enables poliovirus spread between tissues through optimization of the genetic composition of low frequency variants, which together cooperate to circumvent tissue-specific challenges. Thus, intrahost virus evolution determines pathogenesis, allowing a dynamic regulation of viral functions required to overcome barriers to infection.
Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer
Authors: Asim Mohammad , Tarish Firas , Zecchini Heather I. , Sanjiv Kumar , Gelali Eleni , Massie Charles E. , Baridi Ajoeb , Warren Anne Y. , Zhao Wanfeng , Ogris Christoph , McDuffus Leigh-Anne , Mascalchi Patrice , Shaw Greg , Dev Harveer , Wadhwa Karan , Wijnhoven Paul , Forment Josep V. , Lyons Scott R. , Lynch Andy G. , O’Neill Cormac , Zecchini Vincent R. , Rennie Paul S. , Baniahmad Aria , Tavaré Simon , Mills Ian G. , Galanty Yaron , Crosetto Nicola , Schultz Niklas , Neal David , Helleday Thomas
Published: August 2017

Emerging data demonstrate homologous recombination (HR) defects in castration-resistant prostate cancers, rendering these tumours sensitive to PARP inhibition. Here we demonstrate a direct requirement for the androgen receptor (AR) to maintain HR gene expression and HR activity in prostate cancer. We show that PARP-mediated repair pathways are upregulated in prostate cancer following androgen-deprivation therapy (ADT). Furthermore, upregulation of PARP activity is essential for the survival of prostate cancer cells and we demonstrate a synthetic lethality between ADT and PARP inhibition in vivo. Our data suggest that ADT can functionally impair HR prior to the development of castration resistance and that, this potentially could be exploited therapeutically using PARP inhibitors in combination with androgen-deprivation therapy upfront in advanced or high-risk prostate cancer.
Matrix degradability controls multicellularity of 3D cell migration
Authors: Trappmann Britta , Baker Brendon M. , Polacheck William J. , Choi Colin K. , Burdick Jason A. , Chen Christopher S.
Published: August 2017

A major challenge in tissue engineering is the development of materials that can support angiogenesis, wherein endothelial cells from existing vasculature invade the surrounding matrix to form new vascular structures. To identify material properties that impact angiogenesis, here we have developed an in vitro model whereby molded tubular channels inside a synthetic hydrogel are seeded with endothelial cells and subjected to chemokine gradients within a microfluidic device. To accomplish precision molding of hydrogels and successful integration with microfluidics, we developed a class of hydrogels that could be macromolded and micromolded with high shape and size fidelity by eliminating swelling after polymerization. Using this material, we demonstrate that matrix degradability switches three-dimensional endothelial cell invasion between two distinct modes: single-cell migration and the multicellular, strand-like invasion required for angiogenesis. The ability to incorporate these tunable hydrogels into geometrically constrained settings will enable a wide range of previously inaccessible biomedical applications.
On-chip single photon filtering and multiplexing in hybrid quantum photonic circuits
Authors: Elshaari Ali W. , Zadeh Iman Esmaeil , Fognini Andreas , Reimer Michael E. , Dalacu Dan , Poole Philip J. , Zwiller Val , Jöns Klaus D.
Published: August 2017

Quantum light plays a pivotal role in modern science and future photonic applications. Since the advent of integrated quantum nanophotonics different material platforms based on III–V nanostructures-, colour centers-, and nonlinear waveguides as on-chip light sources have been investigated. Each platform has unique advantages and limitations; however, all implementations face major challenges with filtering of individual quantum states, scalable integration, deterministic multiplexing of selected quantum emitters, and on-chip excitation suppression. Here we overcome all of these challenges with a hybrid and scalable approach, where single III–V quantum emitters are positioned and deterministically integrated in a complementary metal–oxide–semiconductor-compatible photonic circuit. We demonstrate reconfigurable on-chip single-photon filtering and wavelength division multiplexing with a foot print one million times smaller than similar table-top approaches, while offering excitation suppression of more than 95 dB and efficient routing of single photons over a bandwidth of 40 nm. Our work marks an important step to harvest quantum optical technologies’ full potential.
SDE5, a putative RNA export protein, participates in plant innate immunity through a flagellin-dependent signaling pathway in Arabidopsis
Authors: Uddin Mohammad Nazim , Akhter Salina , Chakraborty Rupak , Baek Ji Hyeong , Cha Joon-Yung , Park Su Jung , Kang Hunseung , Kim Woe-Yeon , Lee Sang Yeol , Mackey David , Kim Min Gab
Published: August 2017

In eukaryotes, RNA silencing, mediated by small interfering RNAs, is an evolutionarily widespread and versatile silencing mechanism that plays an important role in various biological processes. Increasing evidences suggest that various components of RNA silencing pathway are involved in plant defense machinery against microbial pathogens in Arabidopsis thaliana. Here, we show genetic and molecular evidence that Arabidopsis SDE5 is required to generate an effective resistance against the biotrophic bacteria Pseudomonas syringae pv. tomato DC3000 and for susceptibility to the necrotrophic bacteria Erwinia caratovora pv. caratovora. SDE5, encodes a putative mRNA export factor that is indispensable for transgene silencing and the production of trans-acting siRNAs. SDE5 expression is rapidly induced by exogenous application of phytohormone salicylic acid (SA), methyl jasmonate (MeJA), phytopathogenic bacteria, and flagellin. We further report that SDE5 is involved in basal plant defense and mRNA export. Our genetic data suggests that SDE5 and Nonexpressor of PR Gene1 (NPR1) may contribute to the same SA-signaling pathway. However, SDE5 over-expressing transgenic plant exhibits reduced defense responsive phenotype after flagellin treatment. Taken together, these results support the conclusion that SDE5 contributes to plant innate immunity in Arabidopsis.
Circadian Clock Model Supports Molecular Link Between PER3 and Human Anxiety
Authors: Liberman Amanda R. , Kwon Soo Bin , Vu Ha T. , Filipowicz Allan , Ay Ahmet , Ingram Krista K.
Published: August 2017

Generalized anxiety and major depression have become increasingly common in the United States, affecting 18.6 percent of the adult population. Mood disorders can be debilitating, and are often correlated with poor general health, life dissatisfaction, and the need for disability benefits due to inability to work. Recent evidence suggests that some mood disorders have a circadian component, and disruptions in circadian rhythms may even trigger the development of these disorders. However, the molecular mechanisms of this interaction are not well understood. Polymorphisms in a circadian clock-related gene, PER3, are associated with behavioral phenotypes (extreme diurnal preference in arousal and activity) and sleep/mood disorders, including seasonal affective disorder (SAD). Here we show that two PER3 mutations, a variable number tandem repeat (VNTR) allele and a single-nucleotide polymorphism (SNP), are associated with diurnal preference and higher Trait-Anxiety scores, supporting a role for PER3 in mood modulation. In addition, we explore a potential mechanism for how PER3 influences mood by utilizing a comprehensive circadian clock model that accurately predicts the changes in circadian period evident in knock-out phenotypes and individuals with PER3-related clock disorders.
The FER rs4957796 TT genotype is associated with unfavorable 90-day survival in Caucasian patients with severe ARDS due to pneumonia
Authors: Hinz José , Büttner Benedikt , Kriesel Fabian , Steinau Maximilian , Frederik Popov Aron , Ghadimi Michael , Beissbarth Tim , Tzvetkov Mladen , Bergmann Ingo , Mansur Ashham
Published: August 2017

A recent genome-wide association study showed that a genetic variant within the FER gene is associated with survival in patients with sepsis due to pneumonia. Because severe pneumonia is the main cause of acute respiratory distress syndrome (ARDS), we aimed to investigate the effect of the FER polymorphism rs4957796 on the 90-day survival in patients with ARDS due to pneumonia. An assessment of a prospectively collected cohort of 441 patients with ARDS admitted to three intensive care units at the University Medical Centre identified 274 patients with ARDS due to pneumonia. The 90-day mortality risk was recorded as the primary outcome parameter. Sepsis-related organ failure assessment (SOFA) scores and organ support-free days were used as the secondary variables. FER rs4957796 TT-homozygous patients were compared with C-allele carriers. The survival analysis revealed a higher 90-day mortality risk among T homozygotes than among C-allele carriers (p = 0.0144) exclusively in patients with severe ARDS due to pneumonia. The FER rs4957796 TT genotype remained a significant covariate for the 90-day mortality risk in the multivariate analysis (hazard ratio, 4.62; 95% CI, 1.58–13.50; p = 0.0050). In conclusion, FER rs4957796 might act as a prognostic variable for survival in patients with severe ARDS due to pneumonia.
Microbial communities with distinct denitrification potential in spruce and beech soils differing in nitrate leaching
Authors: Bárta Jiří , Tahovská Karolina , Šantrůčková Hana , Oulehle Filip
Published: August 2017

Nitrogen leaching owing to elevated acid deposition remains the main ecosystem threat worldwide. We aimed to contribute to the understanding of the highly variable nitrate losses observed in Europe after acid deposition retreat. Our study proceeded in adjacent beech and spruce forests undergoing acidification recovery and differing in nitrate leaching. We reconstructed soil microbial functional characteristics connected with nitrogen and carbon cycling based on community composition. Our results showed that in the more acidic spruce soil with high carbon content, where Acidobacteria and Actinobacteria were abundant (Proteo:Acido = 1.3), the potential for nitrate reduction and loss via denitrification was high (denitrification: dissimilative nitrogen reduction to ammonium (DNRA) = 3). In the less acidic beech stand with low carbon content, but high nitrogen availability, Proteobacteria were more abundant (Proteo:Acido = 1.6). Proportionally less nitrate could be denitrified there (denitrification:DNRA = 1), possibly increasing its availability. Among 10 potential keystone species, microbes capable of DNRA were identified in the beech soil while instead denitrifiers dominated in the spruce soil. In spite of the former acid deposition impact, distinct microbial functional guilds developed under different vegetational dominance, resulting in different N immobilization potentials, possibly influencing the ecosystem’s nitrogen retention ability.
Trace metals and magnetic particles in PM2.5: Magnetic identification and its implications
Authors: Wang Jinhua , Li Shiwei , Li Huiming , Qian Xin , Li Xiaolong , Liu Xuemei , Lu Hao , Wang Cheng , Sun Yixuan
Published: August 2017

Magnetic measurement was combined with geochemical analysis to investigate the trace metal pollution of PM2.5. The study was carried out in Nanjing, China, where the average PM2.5 concentrations in summer and winter in 2013–2014 were 66.37 and 96.92 μg/m3, respectively. The dominant magnetic mineral in PM2.5 had a low-coercivity pseudo-single domain and consisted of magnetite and hematite. Iron-oxide magnetic particles comprised spherical as well as angular particles. Stable Pb isotopic ratio determinations showed that Pb in summer samples derived from coal emissions while the main sources of winter samples were smelting industry and coal emissions. The magnetic properties of the particles correlated strongly with trace metals derived from anthropogenic activities, such as industrial emission, coal combustion, and traffic vehicle activities, but poorly with those derived from natural sources. In the multiple linear regression analysis, Cr and Fe had higher correlation coefficients (training R > 0.7) in contrast to the low training R of As, Cd, Ni, Sr, and Ti (<0.5) determined using the PM2.5 concentrations and magnetic parameter values as the decision variables. Our results support the use of environmental magnetism determinations as a simple and fast method to assess trace metals in urban particulate matter.
Optical Pump Rectification Emission: Route to Terahertz Free-Standing Surface Potential Diagnostics
Authors: Peters L. , Tunesi J. , Pasquazi A. , Peccianti M.
Published: August 2017

We introduce a method for diagnosing the electric surface potential of a semiconductor based on THz surface generation. In our scheme, that we name Optical Pump Rectification Emission, a THz field is generated directly on the surface via surface optical rectification of an ultrashort pulse after which the DC surface potential is screened with a second optical pump pulse. As the THz generation directly relates to the surface potential arising from the surface states, we can then observe the temporal dynamics of the static surface field induced by the screening effect of the photo-carriers. Such an approach is potentially insensitive to bulk carrier dynamics and does not require special illumination geometries.
Reproducibility and differences in area of foveal avascular zone measured by three different optical coherence tomographic angiography instruments
Authors: Shiihara Hideki , Sakamoto Taiji , Yamashita Takehiro , Kakiuchi Naoko , Otsuka Hiroki , Terasaki Hiroto , Sonoda Shozo
Published: August 2017

This study was performed to compare the area of the foveal avascular zone (FAZ-area) obtained by three optical coherence tomography angiography (OCTA) instruments. This was a cross-sectional, non-interventional study of twenty-seven healthy right eyes. The superficial and deep FAZ-area was measured manually with three OCTA instruments: Triton (Topcon), RS3000 (Nidek), and CIRRUS (Zeiss). The intra-rater, inter-rater, and inter-instrument correlation coefficients (CC) were assessed. The intra-rater and inter-rater CC were significantly high for the superficial and deep FAZ-areas (P < 0.001). The inter-instrument CC (95% confidence interval) for the superficial FAZ-area was 0.920 (0.803–0.965) for Triton vs RS3000, 0.899 (0.575–0.965) for RS3000 vs CIRRUS, and was 0.963 (0.913–0.983) for CIRRUS vs Triton (P < 0.001). For the deep FAZ-area, the inter-instrument CC was 0.813 (0.633–0.910) for Triton vs RS3000, 0.694 (0.369–0.857) for RS3000 vs CIRRUS, and 0.679 (0.153–0.872) for CIRRUS vs Triton (P < 0.001). The superficial FAZ-area (mm2) was 0.264 ± 0.071 with Triton, 0.278 ± 0.072 with RS3000 and 0.257 ± 0.066 with CIRRUS. For deep FAZ-area, it was 0.617 ± 0.175 with Triton, 0.646 ± 0.178 with RS3000 and 0.719 ± 0.175 with CIRRUS. The FAZ-area from these instruments was clinically interchangeable. However, the absolute values of FAZ-area are significantly different among them. These differences must be considered in comparing the FAZ-areas from different OCTA instruments.
A Physics-Inspired Mechanistic Model of Migratory Movement Patterns in Birds
Authors: Revell Christopher , Somveille Marius
Published: August 2017

In this paper, we introduce a mechanistic model of migratory movement patterns in birds, inspired by ideas and methods from physics. Previous studies have shed light on the factors influencing bird migration but have mainly relied on statistical correlative analysis of tracking data. Our novel method offers a bottom up explanation of population-level migratory movement patterns. It differs from previous mechanistic models of animal migration and enables predictions of pathways and destinations from a given starting location. We define an environmental potential landscape from environmental data and simulate bird movement within this landscape based on simple decision rules drawn from statistical mechanics. We explore the capacity of the model by qualitatively comparing simulation results to the non-breeding migration patterns of a seabird species, the Black-browed Albatross (Thalassarche melanophris). This minimal, two-parameter model was able to capture remarkably well the previously documented migration patterns of the Black-browed Albatross, with the best combination of parameter values conserved across multiple geographically separate populations. Our physics-inspired mechanistic model could be applied to other bird and highly-mobile species, improving our understanding of the relative importance of various factors driving migration and making predictions that could be useful for conservation.
A study of size-dependent properties of MoS2 monolayer nanoflakes using density-functional theory
Authors: Javaid M. , Drumm Daniel W. , Russo Salvy P. , Greentree Andrew D.
Published: August 2017

Novel physical phenomena emerge in ultra-small sized nanomaterials. We study the limiting small-size-dependent properties of MoS2 monolayer rhombic nanoflakes using density-functional theory on structures of size up to Mo35S70 (1.74 nm). We investigate the structural and electronic properties as functions of the lateral size of the nanoflakes, finding zigzag is the most stable edge configuration, and that increasing size is accompanied by greater stability. We also investigate passivation of the structures to explore realistic settings, finding increased HOMO-LUMO gaps and energetic stability. Understanding the size-dependent properties will inform efforts to engineer electronic structures at the nano-scale.
Putrescine independent wound response phenotype is produced by ODC-like RNAi in planarians
Authors: Cassella Lucia , Salvetti Alessandra , Iacopetti Paola , Ippolito Chiara , Ghezzani Claudio , Gimenez Gregory , Ghigo Eric , Rossi Leonardo
Published: August 2017

Despite increasing evidence indicates polyamines as a convergence point for signaling pathways, including cell growth and differentiation, a unifying concept to interpret their role is still missing. The activity of ornithine decarboxylase (ODC), the rate-limiting enzyme in polyamine biosynthesis, is tightly regulated by a complex molecular machinery, and the demonstration of the existence of multiple ODC paralogs, lacking decarboxylation activity, suggests additional layers of complexity to the intricate ODC regulatory pathway. Because of their extraordinary regenerative abilities and abundance of stem cells, planarians have potential to contribute to our understanding of polyamine function in an in vivo context. We undertook a study on ODC function in planarians and we found six planarian ODCs (ODC1-6). Five out of six ODC homologs carry substitutions of key aminoacids for enzymatic activity, which makes them theoretically unable to decarboxylate ornithine. Silencing of ODC5 and 6 produced a complex phenotype, by prompting animals to an aberrant response, following chronic injury without tissue removal. Phenotype is neither rescued by putrescine, nor mimicked by difluoromethylornithine treatment. Moreover, the co-silencing of other genes of the ODC regulatory pathway did not modulate phenotype outcome or severity, thus suggesting that the function/s of these ODC-like proteins might be unrelated to decarboxylase activity and putrescine production.