bluuebunny/crossref_metadata_2025 huggingface dataset:
Missing Links in Poverty Analysis in the Age of Neoliberal Globalization: Some Lessons from Turkey
Authors: Şenses Fikret
Published: February 2016

The main objective of this essay is to point out the missing links between neoliberalism on the one hand, and a comprehensive analysis of poverty and effective policies to tackle it, on the other. After identifying the main channels through which neoliberalism affects poverty, I will draw attention to the inadequacy of the neoliberal approach in coming to terms with the main reasons behind poverty, as well as in developing a comprehensive and effective mechanism for its alleviation. I emphasize the role of international institutions in determining the dominant development discourse and changes in the importance given to the issue of poverty over time. The essay links the ineffectiveness of existing poverty alleviation policies to distributional imbalances at both the global and domestic levels. Against the background of the main constraints and opportunities for effective poverty alleviation policies in individual countries, it emphasizes the need for a poverty alleviation strategy as an integral part of a broader development strategy and identifies its main premises. It calls for action on the academic, domestic and international fronts and stresses the central role of the state, a more balanced reliance on domestic and international markets, emphasis on productive employment creation, the development of effective redistribution mechanisms, and the creation of effective domestic and international constituencies as the main components of such a strategy.
Community Matters: A Study of the Interaction of Microcredit Borrowers in Diyarbakır with the Market Economy?
Authors: Bulut Tuğçe
Published: February 2016

This paper analyzes the processes of integration of the poor into the market, as instigated by their involvement in microfinance projects. This analysis is based on the findings of an ethnographic study of the Turkish Grameen Microcredit Project (TGMP), conducted in Diyarbakır at different time periods between September of 2004 and July of 2005. By analyzing in detail the nature of economic life revolving around the microfinance practices, this paper intends to elucidate the way in which the integration of the microcredit borrowers into the market is guided by societal processes. The findings of the field research show that in everyday practices the borrowers adjust the microfinance system to their own needs and accommodate the economic activities originating in microcredit into their wider social structure. Thus, one can conclude that they are integrated into the market in their own way, guiding the integration process with their own socio-cultural institutions.
The fight over nobody's children: Religion, nationality and citizenship of foundlings in the late Ottoman Empire
Authors: Maksudyan Nazan
Published: February 2016

In the late nineteenth century, the religion, nationality, and citizenship of abandoned children became a contested terrain over which much effort was spent by local authorities, foreign missionaries, religious and civil leaders of the communities, municipalities, the police force, and the central state. Relying on Ottoman and French archival sources, together with periodicals and contemporary literature, this paper discerns the elevated political significance of abandoned children within such realms as demographic politics, politics of conversion, and national identities. The state's new preoccupation of properly registering new-born infants, in line with the new Regulation on Population Registration created controversy over the nationality and citizenship of abandoned children. As new administrative reforms challenged the customary jurisdiction and the autonomy of the communal authorities and as the power of the governmental bureaus, police departments, the municipality, and the foundling unit of theDârü'l-acezeincreased, non-Muslim leadership resisted these practices: they both submitted official appeals to the government and opened or strengthened their own foundling facilities. Furthermore, the child gathering efforts of Catholic missionaries created an atmosphere of self-defense on the part of the communities, as they felt threatened with losing prospective members of their newly conceived and idealized imagined communities. In this context, abandoned children attracted interest hardly due to pity, or disinterested charity. Institutional solutions, policies, and strategies of diverse and competing actors were closely related to the emergence of a modernized governmental structure and attempts to strengthen communities as its mirror image.
Fruitless Attempts? The Kurdish Initiative and Containment of the Kurdish Movement in Turkey
Authors: Casier Marlies , Jongerden Joost , Walker Nic
Published: February 2016

Following the victory of the Kurdish party DTP (Demokratik Toplum Partisi, Democratic Society Party) in Turkey's southeastern provinces in the local elections of March 2009, Turkey witnessed the AKP (Adalet ve Kalkınma Partisi, Justice and Development Party) government's Kurdish initiative, the closure of the victorious Kurdish party, and waves of arrests of Kurdish activists and politicians. This rush of action constituted a renewed effort to contain and roll back the political and societal influence of the Kurdish movement. But what is it exactly that the government and the state were attempting to contain, and why? This article considers the recent moves of the ruling AKP, the judiciary, and the Turkish Armed Forces in regard to the “Kurdish problem” in Turkey's southeast, interpreting them as different responses to the regional success of the Kurdish movement.
Astray and Stranded at the Gates of The European Union: African Transit Migrants in İstanbul
Authors: Yükseker Deniz , Brewer Kelly Todd
Published: February 2016

This paper discusses the consequences of EU migration control policies on irregular and transit migration in Turkey by focusing on African migrants. Our argument is that the EU's concern with transit migration through the Mediterranean and hence its externalization and securitization of migration control have contributed to Turkey's becoming a waiting room for irregular and transit migrants. Based on the findings of a survey with African migrants in İstanbul and analysis of secondary sources, we show that many African migrants get stranded in Turkey. In the absence of an institutional setup for migration management and the prevalence of a security approach, migrants are faced with humanitarian problems and human rights violations.
Metamorphoses of the “Stranger”: Jews in Europe, Polish Peasants in America, Turks in Germany
Authors: Karakayalı Nedim
Published: February 2016

The increase in population of wood and mountain barbarian tribes on one hand, and the increasing demand for labor in the developing culture areas on the other created, with increasing wealth, numerous lower or unclean services. When the local resident population declined to take them over, these occupations fell into the hands of alien workers of foreign origin who were permanently lodged in urban areas but retained their tribal affiliations (Max Weber, 1968 [1923], p. 12).
Migration From Turkey to Germany: An Ethnic Approach
Authors: Sirkeci İbrahim
Published: February 2016

Ülkemin ırmakları dışarı akar

Neden bilmem can havliyle akar…

(Cemal Süreya, 1988)

(The rivers of my country are flowing out

Frightened to death they flow, I know not why…)

The growth in the numbers of asylum seekers to Western European countries over the past decade (Castles and Loughna, 2002) has underlined the significance of “political” and other non-economic factors in shaping migration flows, drawing attention to the inadequacy of theoretical explanations based on socio-economic differentials. The need to reassess earlier research on labor flows to take into account the existence of migrants obliged to flee from situations involving political persecution has become apparent, whether the migrants be directly or personally a target of persecution or whether they feel threatened by association for reasons of ethnicity, geography, etc. My main aim in this article is to raise the issue of the role of “Kurdish ethnicity” as one instance of such political forces in shaping migration flows from Turkey to Germany. During the 1970s and 1980s, research on patterns of migration between the two countries was almost exclusively concerned with the “incorporation of guest workers” into German labor markets and the contribution of their remittances to the Turkish economy.
Hizmet: A Keyword in the Turkish Historical Narrative
Authors: Copeaux Etienne
Published: February 2016

In the discourse of the history textbooks used since 1931, the relationship between identity and otherness often tends towards the necessity of proving both the value and greatness of Turkish history and culture. Consequently, the whole historical narrative, and also the discourse on identity and the nationalist discourse, which very often make use of history in their argumentation, always present the Turks in a favorable light and in an emphasized role. This appears in several forms, particularly during a kind of reconstruction of the past using tenses expressing the unreal condition (“If the Turks had not existed… Islam could not have been saved”, or “… the European Renaissance could not have taken place”, etc.). Another noticeable form is the use of the word hizmet, (“service”, “utility”, helpfulness”, “function”) provided by the Turks. The word itself is helpful to fit the Turks in with “otherness”, in the way of showing them in a good light in history. With regard to this notion, according to the narrative, wide groups of “others” often take advantage of the existence of the Turks: the whole mankind, the “free world”, or the Muslim world, according to the time when the discourse was formulated.
The Politics of Poor Relief in the Late Ottoman Empire 1876-1914
Authors: Özbek Nadir
Published: February 2016

This article examines the Ottoman state's increasing involvement in caring for the poor and the needy and the emergence of modern relief institutions and hospitals throughout the late nineteenth and early twentieth centuries. The particular focus will be on the reign of Sultan Abdülhamid II (1876-1909) and the second constitutional period (1908-14) up until World War I.

Rather than presenting the emergence of poor-relief institutions in the Ottoman Empire as a function of increasing poverty and need, or as a function of the state's desire to control and regulate the urban population for various concerns, I concentrate on the dynamics of the political sphere. I will focus particularly on the political conflict between the sultan and the new political elite, whose identity was defined in relation to newly structured state functions and services.
Information or Culture: The Intellectual Dissemination of Americanism as Common Sense
Authors: Kaçel Ela
Published: February 2016

The discourse of postwar modern architecture is dominated by historical accounts that easily describe the processes of modernization in Turkey during the Cold War as a unilateral flow of ideas and expertise from the United States. Yet, the relation between benefactor and beneficiary is much more complex. This article explores culture production as a state function and intellectual practice through which bureaucrats and intellectuals representing the state agencies disseminated Americanism as common sense in postwar Turkey. Drawing on the cultural activities of two parallel organizations, the Turkish Information Office (TIO) acting in New York and the United States Information Service (USIS) in Turkey, it illustrates how the intricate relations among ideology, politics, and architecture affect the practices of bureaucrats and their audiences in the process of culture production. Promoting ideologies of Americanism, these organizations simultaneously popularized American architects and their buildings to their audiences. The comparative analysis of two case studies, the photo bookTalking Turkeyby the TIO and the Architecture Series of the Voice of America Forum Lectures, demonstrates how the division created between information and culture as two separate functions of foreign diplomacy perpetuated similar divisions in architectural discourse such as the iconic and the ordinary.
A success story or a flawed example? The anatomy of the Turkish model for the Middle East
Authors: Özdikmenli İlkim , Ovalı Şevket
Published: February 2016

This article argues that it is fallacious to promote the Turkish democratic experience under the Justice and Development Party (Adalet ve Kalkınma Partisi, AKP) as a model for the emerging Arab democracies. Despite the early political reformism of the AKP, an empirical analysis of the government’s recent crackdown on basic rights and freedoms demonstrates that the “Turkish model,” defined as a marriage of Islam and liberal democracy, cannot respond to the demands of Arab reformers. In this regard, the article falls into three sections. In the first section, assets of the “Turkish model” according to various actors are examined, which casts doubt on the emancipatory discourse underlying the promotion of the model. The second section proposes the term “leader democracy”—or, more specifically, “Erdoğanism”—as a way of denoting the governmental structure of Turkey as of early 2014. The final section depicts the current Turkish democracy in terms of the state of checks and balances and of basic political and social rights.
Gypsies in the economy of Turkey: A focus on Gypsy flower sellers in two central districts of İstanbul
Authors: Özateşler Gül
Published: February 2016

This article aims to explore the conditions and roles of Gypsies in the economy of Turkey through a focus on street flower sellers in two central districts of İstanbul, Şişli and Taksim. It proposes a multidimensional analysis that demonstrates different dynamics of social exclusion, socio-economic and political relations, and agency positions. After first reviewing several approaches to Gypsies’ roles in non-Gypsy economies, Gypsies’ conditions in Turkey are then examined in relation to their roles in the economy. Finally, their positions in the flower-selling sector in the two districts, Şişli and Taksim, are analyzed through working conditions, socioeconomic dynamics, social exclusion, and perceptions of Gypsyness.
In vitromaturation alters gene expression in bovine oocytes
Authors: Adona Paulo R. , Leal Cláudia L.V. , Biase Fernando H. , De Bem Tiago H. , Mesquita Lígia G. , Meirelles Flávio V. , Ferraz André L. , Furlan Luiz R. , Monzani Paulo S. , Guemra Samuel
Published: February 2016

Gene expression profiling ofin vivo- andin vitro-matured bovine oocytes can identify transcripts related to the developmental potential of oocytes. Nonetheless, the effects ofin vitroculturing oocytes are yet to be fully understood. We tested the effects ofin vitromaturation on the transcript profile of oocytes collected fromBos taurus indicuscows. We quantified the expression of 1488 genes inin vivo- andin vitro-matured oocytes. Of these, 51 genes were up-regulated, whereas 56 were down-regulated (≥2-fold) inin vivo-matured oocytes in comparison within vitro-matured oocytes. Quantitative real-time polymerase chain reaction (PCR) of nine genes confirmed the microarray results of differential expression betweenin vivo- andin vitro-matured oocytes (EZR, EPN1, PSEN2, FST, IGFBP3, RBBP4, STAT3, FDPSandIRS1). We interrogated the results for enrichment of Gene Ontology categories and overlap with protein–protein interactions. The results revealed that the genes altered byin vitromaturation are mostly related to the regulation of oocyte metabolism. Additionally, analysis of protein–protein interactions uncovered two regulatory networks affected by thein vitroculture system. We propose that the differentially expressed genes are candidates for biomarkers of oocyte competence.In vitrooocyte maturation can affect the abundance of specific transcripts and are likely to deplete the developmental competence.
Automobile usage and urban rail transit expansion: evidence from a natural experiment in Beijing, China
Authors: Xie Lunyu
Published: February 2016

Using individual travel diary data collected before and after a rail transit expansion in urban Beijing, the impact of urban rail accessibility improvement on the usage of rail transit, automobiles, buses, walking and bicycling, as well as the cross-area externality induced by congestion alleviation, is estimated. The results show that rail transit usage significantly increased for commuters residing in the affected areas and that the additional rail passengers were previously auto users, rather than bus passengers. The cross-area externality is estimated as small, which implies that the congestion alleviation was not large enough (yet) to change the travel mode choices of commuters residing in areas that did not experience the improvement. Furthermore, the results show that neither the number of commute work trips nor their length increased, indicating that the quantity of travel was not increased by the rail transit expansion.
HISTORICAL BACKTESTING OF LOCAL VOLATILITY MODEL USING AUD/USD VANILLA OPTIONS
Authors: LING T. G. , SHEVCHENKO P. V.
Published: February 2016

The local volatility model is a well-known extension of the Black–Scholes constant volatility model, whereby the volatility is dependent on both time and the underlying asset. This model can be calibrated to provide a perfect fit to a wide range of implied volatility surfaces. The model is easy to calibrate and still very popular in foreign exchange option trading. In this paper, we address a question of validation of the local volatility model. Different stochastic models for the underlying asset can be calibrated to provide a good fit to the current market data, which should be recalibrated every trading date. A good fit to the current market data does not imply that the model is appropriate, and historical backtesting should be performed for validation purposes. We study delta hedging errors under the local volatility model using historical data from 2005 to 2011 for the AUD/USD implied volatility. We performed backtests for a range of option maturities and strikes using sticky delta and theoretically correct delta hedging. The results show that delta hedging errors under the standard Black–Scholes model are no worse than those of the local volatility model. Moreover, for the case of in- and at-the-money options, the hedging error for the Black–Scholes model is significantly better.
Medical savings accounts: assessing their impact on efficiency, equity and financial protection in health care
Authors: Wouters Olivier J. , Cylus Jonathan , Yang Wei , Thomson Sarah , McKee Martin
Published: February 2016

Medical savings accounts (MSAs) allow enrolees to withdraw money from earmarked funds to pay for health care. The accounts are usually accompanied by out-of-pocket payments and a high-deductible insurance plan. This article reviews the association of MSAs with efficiency, equity, and financial protection. We draw on evidence from four countries where MSAs play a significant role in the financing of health care: China, Singapore, South Africa, and the United States of America. The available evidence suggests that MSA schemes have generally been inefficient and inequitable and have not provided adequate financial protection. The impact of these schemes on long-term health-care costs is unclear. Policymakers and others proposing the expansion of MSAs should make explicit what they seek to achieve given the shortcomings of the accounts.
Sarkoidose – klinische Aspekte
Authors: Kleiner Rebekka , Brutsche Martin
Published: February 2016

Zusammenfassung. Die Sarkoidose ist eine pneumotrope granulomatöse Systemerkrankung unklarer Ursache. Die Diagnose einer Sarkoidose basiert auf der klinischen Präsentation und dem histologischen Nachweis von nicht-nekrotisierenden epitheloidzelligen Granulomen – nach Ausschluss anderer Differentialdiagnosen. In > 90 % der Fälle findet sich ein intrathorakaler Befall. Die Diagnosestellung erfolgt deshalb häufig eine Bronchoskopie. Die Indikation zu einer immunosuppressiven Therapie soll aufgrund der mehrheitlich guten Langzeitprognose zurückhaltend gestellt werden.
Disparities in suicide mortality trends between United States of America and 25 European countries: retrospective analysis of WHO mortality database
Authors: Fond Guillaume , Llorca Pierre-Michel , Boucekine Mohamed , Zendjidjian Xavier , Brunel Lore , Lancon Christophe , Auquier Pascal , Boyer Laurent
Published: February 2016

The objective was to examine changes in temporal trends in suicide mortality in 26 Western countries by retrospective trend analysis of the WHO mortality database on causes of deaths. From 1990 to 2010, there was a median reduction in suicide mortality of 22.7%, ranging from a 46% reduction in Estonia to a 26.2% increase in Romania. Suicide mortality decreased by ≥20% in 15 countries and the reduction tended to be greater in countries with higher mortality in 1990. In most of the central European countries mortality strongly declined. The median changes in the age groups were −25.3% (range −62.9% to 72.6%) in people aged 15–24 years, −36.9% (−60.5% to 32.4%) in 25–34 years, −3.6% (−57.1% to 92%) in 35–54 years, −12.2% (−37% to 65,7%) in 55–74 years and −16.1% (−54.5% to 166.7%) in ≥75 years. Suicide prevention programs in youths and in the elderly seem to be effective (at least in females for the elderly) and efforts should be pursued in this way. However, suicide mortality of the people aged 35–54 years has increased in half of the studied countries between 1990 and 2010. Public policies should further orientate their efforts toward this population.
Coexistence of multiple metastable polytypes in rhombohedral bismuth
Authors: Shu Yu , Hu Wentao , Liu Zhongyuan , Shen Guoyin , Xu Bo , Zhao Zhisheng , He Julong , Wang Yanbin , Tian Yongjun , Yu Dongli
Published: February 2016

Derivative structural polytypes coexisting with the rhombohedral A7 structure of elemental bismuth (Bi) have been discovered at ambient condition, based on microstructure analyses of pure Bi samples treated under high pressure and high temperature conditions. Three structures with atomic positions close to those of the A7 structure have been identified through first-principles calculations, showing these polytypes energetically comparable to the A7 structure under ambient condition. Simulated diffraction data are in excellent agreement with the experimental observations. We argue that previously reported some variations of physical properties (e.g., density, electrical conductivity and magnetism) in bismuth could be due to the formation of these polytypes. The coexistence of metastable derivative structural polytypes may be a widely occurring phenomenon in other elemental materials.
Controlling herding in minority game systems
Authors: Zhang Ji-Qiang , Huang Zi-Gang , Wu Zhi-Xi , Su Riqi , Lai Ying-Cheng
Published: February 2016

Resource allocation takes place in various types of real-world complex systems such as urban traffic, social services institutions, economical and ecosystems. Mathematically, the dynamical process of resource allocation can be modeled as minority games. Spontaneous evolution of the resource allocation dynamics, however, often leads to a harmful herding behavior accompanied by strong fluctuations in which a large majority of agents crowd temporarily for a few resources, leaving many others unused. Developing effective control methods to suppress and eliminate herding is an important but open problem. Here we develop a pinning control method, that the fluctuations of the system consist of intrinsic and systematic components allows us to design a control scheme with separated control variables. A striking finding is the universal existence of an optimal pinning fraction to minimize the variance of the system, regardless of the pinning patterns and the network topology. We carry out a generally applicable theory to explain the emergence of optimal pinning and to predict the dependence of the optimal pinning fraction on the network topology. Our work represents a general framework to deal with the broader problem of controlling collective dynamics in complex systems with potential applications in social, economical and political systems.
Identification of Mouse Mesenteric and Subcutaneous in vitro Adipogenic Cells
Authors: Miyata Yugo , Otsuki Michio , Kita Shunbun , Shimomura Iichiro
Published: February 2016

Fat accumulation and the dysfunction of visceral white adipose tissue (WAT), but not subcutaneous WAT, cause abnormalities in whole body metabolic homeostasis. However, no current drugs specifically target visceral WAT. The primary reason for this is that a practical in vitro culture system for mesenteric adipocytes has not been established. To resolve this issue, we sought to identify in vitro adipogenic cells in mesenteric and subcutaneous WATs. First, we examined the expression pattern of surface antigens in stromal-vascular fraction (SVF) cells from mouse mesenteric and subcutaneous WATs, and found the expression of 30 stem cell-related surface antigens. Then, to evaluate the adipogenic ability of each fraction, we performed in vitro screening, and identified five candidate markers for mesenteric adipogenic cells and one candidate marker for subcutaneous adipogenic cells. To investigate whether in vitro adipogenic ability accurately reflects the conditions in vivo, we performed transplantation experiments, and identified CD9− CD201+ Sca-1− cells and CD90+ cells as mesenteric and subcutaneous in vitro adipogenic cells, respectively. Furthermore, mature adipocytes derived from mesenteric and subcutaneous adipogenic cells maintained each characteristic phenotype in vitro. Thus, our study should contribute to the development of a useful culture system for visceral adipocytes.
Synergistic interactions of blood-borne immune cells, fibroblasts and extracellular matrix drive repair in an in vitro peri-implant wound healing model
Authors: Burkhardt Melanie A , Waser Jasmin , Milleret Vincent , Gerber Isabel , Emmert Maximilian Y , Foolen Jasper , Hoerstrup Simon P , Schlottig Falko , Vogel Viola
Published: February 2016

Low correlations of cell culture data with clinical outcomes pose major medical challenges with costly consequences. While the majority of biomaterials are tested using in vitro cell monocultures, the importance of synergistic interactions between different cell types on paracrine signalling has recently been highlighted. In this proof-of-concept study, we asked whether the first contact of surfaces with whole human blood could steer the tissue healing response. This hypothesis was tested using alkali-treatment of rough titanium (Ti) surfaces since they have clinically been shown to improve early implant integration and stability, yet blood-free in vitro cell cultures poorly correlated with in vivo tissue healing. We show that alkali-treatment, compared to native Ti surfaces, increased blood clot thickness, including platelet adhesion. Strikingly, blood clots with entrapped blood cells in synergistic interactions with fibroblasts, but not fibroblasts alone, upregulated the secretion of major factors associated with fast healing. This includes matrix metalloproteinases (MMPs) to break down extracellular matrix and the growth factor VEGF, known for its angiogenic potential. Consequently, in vitro test platforms, which consider whole blood-implant interactions, might be superior in predicting wound healing in response to biomaterial properties.
Astrocyte-derived phosphatidic acid promotes dendritic branching
Authors: Zhu Yan-Bing , Gao Weizhen , Zhang Yongbo , Jia Feng , Zhang Hai-Long , Liu Ying-Zi , Sun Xue-Fang , Yin Yuhua , Yin Dong-Min
Published: February 2016

Astrocytes play critical roles in neural circuit formation and function. Recent studies have revealed several secreted and contact-mediated signals from astrocytes which are essential for neurite outgrowth and synapse formation. However, the mechanisms underlying the regulation of dendritic branching by astrocytes remain elusive. Phospholipase D1 (PLD1), which catalyzes the hydrolysis of phosphatidylcholine (PC) to generate phosphatidic acid (PA) and choline, has been implicated in the regulation of neurite outgrowth. Here we showed that knockdown of PLD1 selectively in astrocytes reduced dendritic branching of neurons in neuron-glia mixed culture. Further studies from sandwich-like cocultures and astrocyte conditioned medium suggested that astrocyte PLD1 regulated dendritic branching through secreted signals. We later demonstrated that PA was the key mediator for astrocyte PLD1 to regulate dendritic branching. Moreover, PA itself was sufficient to promote dendritic branching of neurons. Lastly, we showed that PA could activate protein kinase A (PKA) in neurons and promote dendritic branching through PKA signaling. Taken together, our results demonstrate that astrocyte PLD1 and its lipid product PA are essential regulators of dendritic branching in neurons. These results may provide new insight into mechanisms underlying how astrocytes regulate dendrite growth of neurons.
A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries)
Authors: Ren Xue , Yang Guang-Li , Peng Wei-Feng , Zhao Yong-Xin , Zhang Min , Chen Ze-Hui , Wu Fu-An , Kantanen Juha , Shen Min , Li Meng-Hua
Published: February 2016

Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0–133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.
Engineering long shelf life multi-layer biologically active surfaces on microfluidic devices for point of care applications
Authors: Asghar Waseem , Yuksekkaya Mehmet , Shafiee Hadi , Zhang Michael , Ozen Mehmet O. , Inci Fatih , Kocakulak Mustafa , Demirci Utkan
Published: February 2016

Although materials and engineered surfaces are broadly utilized in creating assays and devices with wide applications in diagnostics, preservation of these immuno-functionalized surfaces on microfluidic devices remains a significant challenge to create reliable repeatable assays that would facilitate patient care in resource-constrained settings at the point-of-care (POC), where reliable electricity and refrigeration are lacking. To address this challenge, we present an innovative approach to stabilize surfaces on-chip with multiple layers of immunochemistry. The functionality of microfluidic devices using the presented method is evaluated at room temperature for up to 6-month shelf life. We integrated the preserved microfluidic devices with a lensless complementary metal oxide semiconductor (CMOS) imaging platform to count CD4+T cells from a drop of unprocessed whole blood targeting applications at the POC such as HIV management and monitoring. The developed immunochemistry stabilization method can potentially be applied broadly to other diagnostic immuno-assays such as viral load measurements, chemotherapy monitoring and biomarker detection for cancer patients at the POC.
The CodY regulator is essential for virulence in Streptococcus suis serotype 2
Authors: Feng Liping , Zhu Jiawen , Chang Haitao , Gao Xiaoping , Gao Cheng , Wei Xiaofeng , Yuan Fangyan , Bei Weicheng
Published: February 2016

The main role of CodY, a global regulatory protein in most low G + C gram-positive bacteria, is in transcriptional repression. To study the functions of CodY in Streptococcus suis serotype 2 (S. suis 2), a mutant codY clone named ∆codY was constructed to explore the phenotypic variation between ∆codY and the wild-type strain. The result showed that the codY mutation significantly inhibited cell growth, adherence and invasion ability of S. suis 2 to HEp-2 cells. The codY mutation led to decreased binding of the pathogen to the host cells, easier clearance by RAW264.7 macrophages and decreased growth ability in fresh blood of Cavia porcellus. The codY mutation also attenuated the virulence of S. suis 2 in BALB/c mice. Morphological analysis revealed that the codY mutation decreased the thickness of the capsule of S. suis 2 and changed the surface structures analylized by SDS-PAGE. Finally, the codY mutation altered the expressions of many virulence related genes, including sialic acid synthesis genes, leading to a decreased sialic acid content in capsule. Overall, mutation of codY modulated bacterial virulence by affecting the growth and colonization of S. suis 2, and at least via regulating sialic acid synthesis and capsule thickness.
HIV coreceptor tropism determination and mutational pattern identification
Authors: Shen Hui-Shuang , Yin Jason , Leng Fei , Teng Rui-Fang , Xu Chao , Xia Xia-Yu , Pan Xian-Ming
Published: February 2016

In the early stages of infection, Human Immunodeficiency Virus Type 1 (HIV-1) generally selects CCR5 as the primary coreceptor for entering the host cell. As infection progresses, the virus evolves and may exhibit a coreceptor-switch to CXCR4. Accurate determination coreceptor usage and identification key mutational patterns associated tropism switch are essential for selection of appropriate therapies and understanding mechanism of coreceptor change. We developed a classifier composed of two coreceptor-specific weight matrices (CMs) based on a full-scale dataset. For this classifier, we found an AUC of 0.97, an accuracy of 95.21% and an MCC of 0.885 (sensitivity 92.92%; specificity 95.54%) in a ten-fold cross-validation, outperforming all other methods on an independent dataset (13% higher MCC value than geno2pheno and 15% higher MCC value than PSSM). A web server (http://spg.med.tsinghua.edu.cn/CM.html) based on our classifier was provided. Patterns of genetic mutations that occur along with coreceptor transitions were further identified based on the score of each sequence. Six pairs of one-AA mutational patterns and three pairs of two-AA mutational patterns were identified to associate with increasing propensity for X4 tropism. These mutational patterns offered new insights into the mechanism of coreceptor switch and aided in monitoring coreceptor switch.
Reduced Graphene Oxide Thin Film on Conductive Substrates by Bipolar Electrochemistry
Authors: Allagui Anis , Abdelkareem Mohammad Ali , Alawadhi Hussain , Elwakil Ahmed S.
Published: February 2016

Recent years have shown an increased interest in developing manufacturing processes for graphene and its derivatives that consider the environmental impact and large scale cost-effectiveness. However, today’s most commonly used synthesis routes still suffer from their excessive use of harsh chemicals and/or the complexity and financial cost of the process. Furthermore, the subsequent transfer of the material onto a substrate makes the overall process even more intricate and time-consuming. Here we describe a single-step, single-cell preparation procedure of metal-supported reduced graphene oxide (rGO) using the principle of bipolar electrochemistry of graphite in deionized water. Under the effect of an electric field between two stainless steel feeder electrodes, grapheme layers at the anodic pole of the wireless graphite were oxidized into colloidal dispersion of GO, which migrated electrophoretically towards the anodic side of the cell, and deposited in the form of rGO (d(002) = 0.395 nm) by van der Waals forces. For substrates chemically more susceptible to the high anodic voltage, we show that the electrochemical setup can be adapted by placing the latter between the wireless graphite and the stainless steel feeder anode. This method is straightforward, inexpensive, environmentally-friendly, and could be easily scaled up for high yield and large area production of rGO thin films.
Tunable short-wavelength spin wave excitation from pinned magnetic domain walls
Authors: Van de Wiele Ben , Hämäläinen Sampo J. , Baláž Pavel , Montoncello Federico , van Dijken Sebastiaan
Published: February 2016

Miniaturization of magnonic devices for wave-like computing requires emission of short-wavelength spin waves, a key feature that cannot be achieved with microwave antennas. In this paper, we propose a tunable source of short-wavelength spin waves based on highly localized and strongly pinned magnetic domain walls in ferroelectric-ferromagnetic bilayers. When driven into oscillation by a microwave spin-polarized current, the magnetic domain walls emit spin waves with the same frequency as the excitation current. The amplitude of the emitted spin waves and the range of attainable excitation frequencies depend on the availability of domain wall resonance modes. In this respect, pinned domain walls in magnetic nanowires are particularly attractive. In this geometry, spin wave confinement perpendicular to the nanowire axis produces a multitude of domain wall resonances enabling efficient spin wave emission at frequencies up to 100 GHz and wavelengths down to 20 nm. At high frequency, the emission of spin waves in magnetic nanowires becomes monochromatic. Moreover, pinning of magnetic domain wall oscillators onto the same ferroelectric domain boundary in parallel nanowires guarantees good coherency between spin wave sources, which opens perspectives towards the realization of Mach-Zehnder type logic devices and sensors.
Tidal pumping facilitates dissimilatory nitrate reduction in intertidal marshes
Authors: Zheng Yanling , Hou Lijun , Liu Min , Liu Zhanfei , Li Xiaofei , Lin Xianbiao , Yin Guoyu , Gao Juan , Yu Chendi , Wang Rong , Jiang Xiaofen
Published: February 2016

Intertidal marshes are alternately exposed and submerged due to periodic ebb and flood tides. The tidal cycle is important in controlling the biogeochemical processes of these ecosystems. Intertidal sediments are important hotspots of dissimilatory nitrate reduction and interacting nitrogen cycling microorganisms, but the effect of tides on dissimilatory nitrate reduction, including denitrification, anaerobic ammonium oxidation and dissimilatory nitrate reduction to ammonium, remains unexplored in these habitats. Here, we use isotope-tracing and molecular approaches simultaneously to show that both nitrate-reduction activities and associated functional bacterial abundances are enhanced at the sediment-tidal water interface and at the tide-induced groundwater fluctuating layer. This pattern suggests that tidal pumping may sustain dissimilatory nitrate reduction in intertidal zones. The tidal effect is supported further by nutrient profiles, fluctuations in nitrogen components over flood-ebb tidal cycles and tidal simulation experiments. This study demonstrates the importance of tides in regulating the dynamics of dissimilatory nitrate-reducing pathways and thus provides new insights into the biogeochemical cycles of nitrogen and other elements in intertidal marshes.
Fire blight disease reactome: RNA-seq transcriptional profile of apple host plant defense responses to Erwinia amylovora pathogen infection
Authors: Kamber Tim , Buchmann Jan P. , Pothier Joël F. , Smits Theo H. M. , Wicker Thomas , Duffy Brion
Published: February 2016

The molecular basis of resistance and susceptibility of host plants to fire blight, a major disease threat to pome fruit production globally, is largely unknown. RNA-sequencing data from challenged and mock-inoculated flowers were analyzed to assess the susceptible response of apple to the fire blight pathogen Erwinia amylovora. In presence of the pathogen 1,080 transcripts were differentially expressed at 48 h post inoculation. These included putative disease resistance, stress, pathogen related, general metabolic, and phytohormone related genes. Reads, mapped to regions on the apple genome where no genes were assigned, were used to identify potential novel genes and open reading frames. To identify transcripts specifically expressed in response to E. amylovora, RT-PCRs were conducted and compared to the expression patterns of the fire blight biocontrol agent Pantoea vagans strain C9-1, another apple pathogen Pseudomonas syringae pv. papulans, and mock inoculated apple flowers. This led to the identification of a peroxidase superfamily gene that was lower expressed in response to E. amylovora suggesting a potential role in the susceptibility response. Overall, this study provides the first transcriptional profile by RNA-seq of the host plant during fire blight disease and insights into the response of susceptible apple plants to E. amylovora.
Immobilization of multivalent glycoprobes on gold surfaces for sensing proteins and macrophages
Authors: Gade Madhuri , Khandelwal Puneet , Sangabathuni Sivakoti , Bavireddi Harikrishna , Murthy Raghavendra Vasudeva , Poddar Pankaj , Kikkeri Raghavendra
Published: February 2016

A non-covalent host–guest strategy to immobilize heptavalent glyco-β-cyclodextrin on gold-coated glass slides to study multivalent carbohydrate–protein interactions is described.
Structure determination of the rutile-TiO2(110)-(1 × 2) surface using total-reflection high-energy positron diffraction (TRHEPD)
Authors: Mochizuki I. , Ariga H. , Fukaya Y. , Wada K. , Maekawa M. , Kawasuso A. , Shidara T. , Asakura K. , Hyodo T.
Published: February 2016

Detailed structure of the rutile-TiO2(110)-(1 × 2) has been determined using the newly developed technique of total-reflection high-energy positron diffraction (TRHEPD).
Effects of ligand and guest solvent molecules on the luminescence properties of Tb : Eu-codoped indium-based MOFs
Authors: Yan Wenbo , Wang Le , Yangxiao Kete , Fu Zhixing , Wu Tao
Published: February 2016

A ligand with its triplet state located between the excited states of the Tb and Eu ions shows effective facilitation in the energy transfer process between them, and the energy transfer process in this case is also influenced by polar guest solvent molecules.
Injectable peptide hydrogels for controlled-release of opioids
Authors: Martin Charlotte , Oyen Edith , Mangelschots Jeroen , Bibian Mathieu , Ben Haddou Tanila , Andrade Jessica , Gardiner James , Van Mele Bruno , Madder Annemieke , Hoogenboom Richard , Spetea Mariana , Ballet Steven
Published: February 2016

Peptide-based hydrogels as a drug carrier system for the subcutaneous administration of morphine.
Review on the Raman spectroscopy of different types of layered materials
Authors: Zhang Xin , Tan Qing-Hai , Wu Jiang-Bin , Shi Wei , Tan Ping-Heng
Published: February 2016

Raman spectroscopy continues to stimulate the explorations on different types of layered materials.
Cryptotanshinone inhibits proliferation and induces apoptosis via mitochondria-derived reactive oxygen species involving FOXO1 in estrogen receptor-negative breast cancer Bcap37 cells
Authors: Liu Xiaoman , Pan Lili , Liang Junling , Li Jinhui , Wu Shihua
Published: February 2016

Cryptotanshinone inhibits proliferation and induces apoptosis of the estrogen receptor-negative breast cancer Bcap37 cells via FOXO1 inhibition and ROS-mediated PI3K/AKT/mTOR signaling pathways.
Facile preparation of bridged silsesquioxane microspheres with interconnected multi-cavities and open holes
Authors: Wang Zhen , Qian Zhenchao , Cao Yuan , Zhang Xiangzhi , Tai Renzhong , Dong Haixia , Zhao Ning , Xu Jian
Published: February 2016

Bridged silsesquioxane (BSQ) microspheres featured with interconnected multi-cavities and open holes are facilely prepared from water-in-oil-in-water emulsion.
Polysaccharide based superabsorbent hydrogel from Mimosa pudica: swelling–deswelling and drug release
Authors: Muhammad Gulzar , Hussain Muhammad Ajaz , Ashraf Muhammad Umer , Haseeb Muhammad Tahir , Hussain Syed Zajif , Hussain Irshad
Published: February 2016

Polysaccharide based stimuli responsive, superporous and superabsorbent hydrogel for sustained drug release.
Predicting 1,3,5,7-tetrakis(4-aminophenyl)adamantine based covalent-organic frameworks as hydrogen storage materials
Authors: Li Xiao-Dong , Feng Shi-Quan , Guo Feng , Liu Xiu-Ying , Yu Jing-Xin , Hou Zhi-Wei
Published: February 2016

Four types of 1,3,5,7-tetrakis(4-aminophenyl)adamantine based covalent-organic frameworks (tapa-COFs) have been designed with topologies of dia, ctn and bor and proposed as high-capacity hydrogen storage materials.
Electron transport study on functionalized armchair graphene nanoribbons: DFT calculations
Authors: Gracia-Espino E. , López-Urías F. , Terrones H. , Terrones M.
Published: February 2016

Quantum transport studies are performed on doped (boron, nitrogen, oxygen, silicon, phosphorus, and sulfur) and functionalized (borane, amine, hydroxyl, thiol, silane, silene, phosphine, and phosphorane) armchair graphene nanoribbons by means of density functional theory.
Molybdenum disulfide nanoflakes through Li-AHA assisted exfoliation in an aqueous medium
Authors: Bindhu B. , Sharu B. K. , Gopika M. S. , Praseetha P. K. , Veluraja K.
Published: February 2016

A novel route to synthesize MoS2 nanoflakes though Li-AHA assisted liquid phase exfoliation.
Pyrazino[2,3-g]quinoxaline-2,7-dione based π-conjugated polymers with affinity towards acids and semiconductor performance in organic thin film transistors
Authors: Quinn Jesse , Guo Chang , Ko Lewis , Sun Bin , He Yinghui , Li Yuning
Published: February 2016

Pyrazino[2,3-g]quinoxaline-2,7-dione (PQx) is used as a building block for π-conjugated polymer semiconductors that demonstrate a strong acid affinity and ambipolar semiconductor performance in thin film transistors.
N-Hydroxyphthalimide catalysts as bioactive pro-oxidants
Authors: Melone L. , Tarsini P. , Candiani G. , Punta C.
Published: February 2016

N-Hydroxyphthalimide organocatalysts bearing lipophilic moieties exhibit a cytotoxic action by promoting oxidative stress in cells.
Thiolate-protected golden fullerenes. A 32-ve core involving a hollow Au32cage
Authors: Rauhalahti M. , Muñoz-Castro A. , Sundholm D.
Published: February 2016

We have computationally investigated the possible formation of large hollow gold nanostructures based on a Au32core covered with a thiolate layer using relativistic density functional theory calculations.
Water vs. cucurbituril rim: a fierce competition for guest solvation
Authors: Ling Xiaoxi , Saretz Stefan , Xiao Lifeng , Francescon John , Masson Eric
Published: February 2016

Remote substituents on cucurbit[7]uril-bound guests are used to decipher the fierce competition between water and the carbonylated portal of the macrocycle for guest stabilization.
A novel donor–acceptor carbazole and benzothiadiazole material for deep red and infrared emitting applications
Authors: Ledwon Przemyslaw , Zassowski Pawel , Jarosz Tomasz , Lapkowski Mieczyslaw , Wagner Pawel , Cherpak Vladyslav , Stakhira Pavlo
Published: February 2016

A novel organic material (C1) with the structure D–π–A–π–D was synthesised and characterised OLEDs based on C1 were fabricated.
Segmented flow sampling with push–pull theta pipettes
Authors: Saha-Shah Anumita , Green Curtis M. , Abraham David H. , Baker Lane A.
Published: February 2016

We report development of a mobile and easy-to-fabricate theta pipette microfluidic device for segmented flow sampling.
A tunable Au core–Ag shell nanoparticle tip for tip-enhanced spectroscopy
Authors: Kim Woong , Kim Nara , Lee Eunbyoul , Kim Duckhoe , Hwan Kim Zee , Won Park Joon
Published: February 2016

A single Au nanoparticle (NP) with a diameter of 5 nm was transferred to the end of a Si-tip through a picking process, and an Ag shell with a controlled thickness was formed on the Au core.