bluuebunny/crossref_metadata_2025 huggingface dataset:
Strategies to reduce plate waste in primary schools – experimental evaluation
Authors: Liz Martins Margarida , Rodrigues Sara SP , Cunha Luís M , Rocha Ada
Published: October 2015

Objective

To determine and compare the effect of two interventions in reducing the plate waste of school lunches.

Design

A between-group analysis was conducted among children from three primary schools: (i) a group receiving intervention A, designed for children and focusing on nutrition education and food waste; (ii) a group receiving intervention B, intended for teachers and focusing on the causes and consequences of food waste; and (iii) a control group with no intervention. For each child, physical weighing of individual meals and leftovers was performed on three non-consecutive weeks at baseline (T0), 1 week (T1, short term) and 3 months (T2, medium term) following the intervention. Plate waste was recorded for a total of 1742 lunches during 14 d over eight different menus.

Setting

Portuguese public primary schools in the city of Porto.

Subjects

All fourth-grade children (n212) attending the three preselected schools.

Results

After intervention A focusing on nutrition education designed for children, a decrease in soup waste was observed compared with the control group. The effect was greater at T1 (−11·9 (se2·8) %;P<0·001) than at T2 (−5·8 (se4·4) %;P=0·103). The plate waste of identical main dishes decreased strongly at T1 (−33·9 (se4·8) %;P<0·001). However, this effect was not found at T2 (−13·7 (se3·2) %;P<0·001). After intervention B involving teachers, plate waste decreased at T2 (−5·5 (se1·9) % for soup; −5·4 (se2·4) % for identical main dishes).

Conclusions

Nutrition education designed for children was more effective in the short than the medium term. Thus, this kind of intervention was not effective in reducing food waste in the medium term. In contrast, an intervention focusing on teachers revealed better results in the medium term than in the short term.
India – Agricultural Products, DS430
Authors: Carlson Geoffrey
Published: October 2015

This dispute concerned India's import prohibition affecting certain agricultural products from countries reporting Notifiable Avian Influenza to the World Organisation for Animal Health (OIE). India maintains this import prohibition through certain legal instruments concerning Avian Influenza (AI) – the AI Measures.
Bilcon et al. v. Canada
Authors: Chevry Jonathan
Published: October 2015

InBilcon et al.v.Canada, a NAFTA Chapter 11 dispute, the tribunal's majority held Canada liable for breaches of NAFTA Articles 1102 (National Treatment) and 1105 (Minimum Standard of Treatment). Pr. D. McRae – Canada's appointed arbitrator – dissented from both findings.
Social Rights of EU Migrant Citizens: Britain and Germany Compared
Authors: Bruzelius Cecilia , Chase Elaine , Seeleib-Kaiser Martin
Published: October 2015

European migrant citizens and their social rights are strongly contested in British political debate. This article seeks to challenge some common concerns and perceptions regarding the exceptionality of the British welfare state and the alleged ‘costs’ to it from intra-EU migration. The article first provides a brief overview of the foundations for EU citizenship and associated social rights, highlighting the semi-sovereign nature of welfare states in the European Union. It then (i) rejects the significance of the often-claimed difference between contributory and non-contributory welfare states in the context of EU migration; and (ii) challenges concerns about the costs of EU migration. The article contrasts the experiences of Britain and Germany. It concludes by considering how concerns often associated with EU migration can be addressed by improving administrative and state capacities.
Religious Liberty in Indonesia and the Rights of “Deviant” Sects
Authors: Alfitri
Published: October 2015

Although Indonesia has acceded to the International Covenant on Civil and Political Rights and freedom of religion is a mandate of the 1945 Constitution, there is a significant difference between the promise and the practice of religious liberty, especially regarding the rights of sects in Indonesia. The article explores this theme in the context of the Congregation of Ahmadiyah Indonesia, a minority Islamic sect which is not considered as anagama, or official religion, as a case study. This designation has had various discriminatory effects on its adherents, which waters down significantly the guarantee of religious freedom in Indonesia.
Dirty Politics: Public Employees, Private Contractors, and the Development of Nineteenth-Century Trash Collection in Pittsburgh and New Orleans
Authors: Strach Patricia , Sullivan Kathleen
Published: October 2015

Nineteenth-century Pittsburgh and New Orleans were a mess: trash filled the streets impeding travel, hindering commerce, and spreading disease. City officials in Pittsburgh turned to private contractors to collect trash at public expense while in New Orleans they relied on city employees (through the mechanism of widows carts). Like Pittsburgh and New Orleans, nineteenth-century cities faced a mounting garbage problem and, like Pittsburgh, northern cities more often chose contract while southern cities more often chose city collection. In this paper, we look in depth at how Pittsburgh and New Orleans chose contract and city collection, what those solutions looked like in practice, and how these two cases might shed light on the North-South difference. We find that both cities rebuffed offers of assistance that may have led to better trash collection and instead based their collection practices on politics. Moreover, the solutions in practice defied the dichotomous labels of public and private and the assumptions that underlie each.
Who Pays, Who Benefits, Who Decides? Urban Infrastructure in Nineteenth-Century Chicago and Twentieth-Century Phoenix
Authors: Heim Carol E.
Published: October 2015

This article compares the financing of urban infrastructure in nineteenth-century Chicago and twentieth-century Phoenix, highlighting distributional conflicts over the cost of public goods. Using the rich secondary literature on Chicago, particularly Robin Einhorn's book, Property Rules: Political Economy in Chicago, 1833–1872, I explore whether adoption of development impact fees in Phoenix in 1987 represented a transition similar to that in Chicago between 1847 and 1851, when a system of special assessments paid by property owners benefiting from an improvement arose, in contrast to citywide financing of public works for citywide benefit. I examine the history of adoption and implementation of development impact fees, which were intended to “make growth pay for itself” by assessing new development to finance infrastructure it would require, and consider whether the fees resembled Chicago's special assessment system in constituting a privatization of government and in reflecting a view that government should not be used to redistribute. I conclude that models that address the provision of urban infrastructure, such as the Tiebout model, would benefit from greater attention to efforts to shift the cost of public goods over space, time, and social groups or classes in growing communities.
Democratic Like Us? Political Orientation and the Effect of Making Democracy Salient on Anti-Israel Attitude
Authors: Lelkes Yphtach , Malka Ariel , Sheets Penelope
Published: October 2015

Israel is viewed unfavorably among wide segments of the public within several European democracies, despite being regarded itself as a Western democracy. Does drawing attention to Israel's democratic attributes improve views toward Israel? In two surveys with Dutch national samples, anti-Semitic affect, low anti-Arab/Muslim affect, and left-wing political orientation independently predicted anti-Israel sentiment. However, in experiments embedded within the surveys, making salient Israel's democratic attributes had opposite effects on Israel attitude across those on the right and the left – slightly decreasing anti-Israel sentiment among those with a right-wing orientation but slightly increasing anti-Israel sentiment among those with a left-wing orientation. We discuss potential explanations grounded in social psychological theory as well as implications for the strategic communication efforts of groups seeking to influence attitudes toward Israel.
Disclosing Brand Placements in Movies
Authors: van Reijmersdal Eva A.
Published: October 2015

Abstract. Recently, the European Union has decided that disclosures of brand placement are obligatory. However, the effects of such disclosures remain largely unstudied. Departing from theoretical notions of the persuasion knowledge model, this study examined how different types of disclosures and viewer involvement with a movie clip affected attitudes toward the placed brand. In addition, the role of attitude toward the placement as mediator was tested. The study employed a one-factorial (no disclosure, disclosure of source, disclosure of source and intent) between-subjects design using an online survey (N = 191). The results showed that disclosure of both the commercial source and the persuasive intent of brand placement resulted in more negative placement attitudes and in turn in more negative brand attitudes than in the absence of a disclosure. In addition, involvement with the movie moderated the disclosure effects: The brand attitudes of high-involved viewers became more negative via placement attitudes when disclosures were shown, regardless of the type of disclosure. For low-involved viewers, a disclosure of both the commercial source and the persuasive intent was necessary to affect brand attitude negatively via placement attitude. These results show that brand placement disclosures can mitigate persuasion. However, the effects depend on the disclosure type and movie involvement. These findings have important implications for theory, legislation, and practice.
Temporal Considerations for Self-Report Research Using Short Message	Service
Authors: Walsh Erin , Brinker Jay K.
Published: October 2015

Abstract. When using Short Message Service (SMS) as a tool for data collection in psychological research, participants can be contacted at any time. This study examined how sampling frequency and time of day of contact impacted on response rates, response completeness, and response delay in repeated measures data collected via SMS. Eighty-five undergraduate students completed a six-item self-report questionnaire via SMS, in response to 20 SMS prompts sent on a random schedule. One group responded across 2 days, the other on a compressed schedule of 1 day. Overall, there was a high response rate. There was no significant difference in response rate, completeness, and delay of those responding across 1 or 2 days. Timing between prompts did not impact on response behavior. Responses were more likely to be complete if prompts were sent during the working day. The shortest time between prompts was 15 min, however, and use of an undergraduate sample limits generalizability. When conducting repeated measures sampling using SMS, researchers should be aware that more frequent sampling can be associated with poorer data quality, and should aim to collect data during the working day rather than mornings or evenings.
Tropical Deforestation Accelerated Faster Than Initially Thought
Authors: Calderone Julia
Published: October 2015

New satellite-based analysis of forest cover in the humid tropics from 1990 to 2010 contradicts previous estimates of rate of loss.
Synthesis of large-area multilayer hexagonal boron nitride for high material performance
Authors: Kim Soo Min , Hsu Allen , Park Min Ho , Chae Sang Hoon , Yun Seok Joon , Lee Joo Song , Cho Dae-Hyun , Fang Wenjing , Lee Changgu , Palacios Tomás , Dresselhaus Mildred , Kim Ki Kang , Lee Young Hee , Kong Jing
Published: October 2015

Although hexagonal boron nitride (h-BN) is a good candidate for gate-insulating materials by minimizing interaction from substrate, further applications to electronic devices with available two-dimensional semiconductors continue to be limited by flake size. While monolayer h-BN has been synthesized on Pt and Cu foil using chemical vapour deposition (CVD), multilayer h-BN is still absent. Here we use Fe foil and synthesize large-area multilayer h-BN film by CVD with a borazine precursor. These films reveal strong cathodoluminescence and high mechanical strength (Young’s modulus: 1.16±0.1 TPa), reminiscent of formation of high-quality h-BN. The CVD-grown graphene on multilayer h-BN film yields a high carrier mobility of ∼24,000 cm2 V−1 s−1 at room temperature, higher than that (∼13,000 2 V−1 s−1) with exfoliated h-BN. By placing additional h-BN on a SiO2/Si substrate for a MoS2 (WSe2) field-effect transistor, the doping effect from gate oxide is minimized and furthermore the mobility is improved by four (150) times.
Ndrg1 is a T-cell clonal anergy factor negatively regulated by CD28 costimulation and interleukin-2
Authors: Oh Yu Mi , Park Hyung Bae , Shin Jae Hun , Lee Ji Eun , Park Ha Young , Kho Dhong Hyo , Lee Jun Sung , Choi Heonsik , Okuda Tomohiko , Kokame Koichi , Miyata Toshiyuki , Kim In-Hoo , Lee Seung Hoon , Schwartz Ronald H. , Choi Kyungho
Published: October 2015

Induction of T-cell clonal anergy involves serial activation of transcription factors, including NFAT and Egr2/3. However, downstream effector mechanisms of these transcription factors are not fully understood yet. Here we identify Ndrg1 as an anergy factor induced by Egr2. Ndrg1 is upregulated by anergic signalling and maintained at high levels in resting anergic T cells. Overexpression of Ndrg1 mimics the anergic state and knockout of the gene prevents anergy induction. Interestingly, Ndrg1 is phosphorylated and degraded by CD28 signalling in a proteasome-dependent manner, explaining the costimulation dependence of anergy prevention. Similarly, IL-2 treatment of anergic T cells, under conditions that lead to the reversal of anergy, also induces Ndrg1 phosphorylation and degradation. Finally, older Ndrg1-deficient mice show T-cell hyperresponsiveness and Ndrg1-deficient T cells aggravate inducible autoimmune inflammation. Thus, Ndrg1 contributes to the maintenance of clonal anergy and inhibition of T-cell-mediated inflammation.
Mussel adhesion is dictated by time-regulated secretion and molecular conformation of mussel adhesive proteins
Authors: Petrone Luigi , Kumar Akshita , Sutanto Clarinda N. , Patil Navinkumar J. , Kannan Srinivasaraghavan , Palaniappan Alagappan , Amini Shahrouz , Zappone Bruno , Verma Chandra , Miserez Ali
Published: October 2015

Interfacial water constitutes a formidable barrier to strong surface bonding, hampering the development of water-resistant synthetic adhesives. Notwithstanding this obstacle, the Asian green mussel Perna viridis attaches firmly to underwater surfaces via a proteinaceous secretion (byssus). Extending beyond the currently known design principles of mussel adhesion, here we elucidate the precise time-regulated secretion of P. viridis mussel adhesive proteins. The vanguard 3,4-dihydroxy-L-phenylalanine (Dopa)-rich protein Pvfp-5 acts as an adhesive primer, overcoming repulsive hydration forces by displacing surface-bound water and generating strong surface adhesion. Using homology modelling and molecular dynamics simulations, we find that all mussel adhesive proteins are largely unordered, with Pvfp-5 adopting a disordered structure and elongated conformation whereby all Dopa residues reside on the protein surface. Time-regulated secretion and structural disorder of mussel adhesive proteins appear essential for optimizing extended nonspecific surface interactions and byssus’ assembly. Our findings reveal molecular-scale principles to help the development of wet-resistant adhesives.
Human caspase-4 and caspase-5 regulate the one-step non-canonical inflammasome activation in monocytes
Authors: Viganò Elena , Diamond Catherine Emma , Spreafico Roberto , Balachander Akhila , Sobota Radoslaw M. , Mortellaro Alessandra
Published: October 2015

Monocytes promote the early host response to infection releasing key pro-inflammatory cytokines, such as IL-1β. The biologically inactive IL-1β precursor is processed to active form by inflammasomes, multi-protein complexes activating caspase-1. Human monocytes exhibit an unconventional one-step pathway of inflammasome activation in response to lipopolysaccharide (LPS) alone. Although this lineage-restricted mechanism is likely to contribute to the pathology of endotoxin shock, signalling pathways regulating this mechanism are currently unknown. Here we report that caspase-4 and caspase-5 mediate IL-1α and IL-1β release from human monocytes after LPS stimulation. Although caspase-4 remains uncleaved, caspase-5 undergoes rapid processing upon LPS treatment. We also identify an additional caspase-5 cleavage product in LPS-stimulated monocytes, which correlates with IL-1 secretion. This one-step pathway requires Syk activity and Ca2+ flux instigated by CD14/TLR4-mediated LPS internalization. Identification of caspase-4/5 as the key determinants of one-step inflammasome activation in human monocytes provides potential targets for therapeutic intervention in endotoxin shock.
Alternative application of Tau protein in Creutzfeldt-Jakob disease diagnosis: Improvement for weakly positive 14-3-3 protein in the laboratory
Authors: Hyeon Jae Wook , Kim Su Yeon , Lee Jeongmin , Park Jun Sun , Hwang Kyu Jam , Lee Sol Moe , An SeongSoo A. , Lee Myung Koo , Ju Young Ran
Published: October 2015

The 14-3-3 protein has been used as a biomarker for the diagnosis of sporadic Creutzfeldt-Jakob disease (sCJD). However, weakly positive 14-3-3 leads to false positive results and an incorrect diagnosis. We attempted to use quantitative data for tau protein to provide an accurate diagnosis based on weak 14-3-3 protein. Sixty-two patients with sCJD, including pathologically confirmed, clinically definite and probable cases and 89 non-CJD patients were investigated based on a Korean population. Among them, 20 sCJD and 14 non-CJD showed weakly positive 14-3-3. The total tau (t-tau) and phosphorylated tau (p-tau) protein levels were measured by ELISA and the p-tau to t-tau ratio (p/t ratio) was calculated. The combined use of the 14-3-3 protein assay, t-tau levels and p/t ratio improved the specificity of diagnosis compared with the use of the 14-3-3 protein assay alone (47% for 14-3-3 alone; 85.94% for 14-3-3 combined with t-tau; 90.62% for 14-3-3 combined with the p/t ratio). In addition, 18 of 20 sCJD and 12 of 14 non-CJD who were weakly positive for 14-3-3 were positive for the p/t ratio and negative for the p/t ratio, respectively. When used in combination with the 14-3-3 protein, the tau protein is useful as a biomarker for the precise diagnosis of sCJD.
Sexual behavior, risk perception and HIV transmission can respond to HIV antiviral drugs and vaccines through multiple pathways
Authors: Tully Stephen , Cojocaru Monica , Bauch Chris T.
Published: October 2015

There has been growing use of highly active antiretroviral treatment (HAART) for HIV and significant progress in developing prophylactic HIV vaccines. The simplest theories of counterproductive behavioral responses to such interventions tend to focus on single feedback mechanisms: for instance, HAART optimism makes infection less scary and thus promotes risky sexual behavior. Here, we develop an agent based, age-structured model of HIV transmission, risk perception and partner selection in a core group to explore behavioral responses to interventions. We find that interventions can activate not one, but several feedback mechanisms that could potentially influence decision-making and HIV prevalence. In the model, HAART increases the attractiveness of unprotected sex, but it also increases perceived risk of infection and, on longer timescales, causes demographic impacts that partially counteract HAART optimism. Both HAART and vaccination usually lead to lower rates of unprotected sex on the whole, but intervention effectiveness depends strongly on whether individuals over- or under-estimate intervention coverage. Age-specific effects cause sexual behavior and HIV prevalence to change in opposite ways in old and young age groups. For complex infections like HIV—where interventions influence transmission, demography, sexual behavior and risk perception—we conclude that evaluations of behavioral responses should consider multiple feedback mechanisms.
Shortcuts to adiabatic passage for fast generation of Greenberger-Horne-Zeilinger states by transitionless quantum driving
Authors: Chen Ye-Hong , Xia Yan , Song Jie , Chen Qing-Qin
Published: October 2015

Berry’s approach on “transitionless quantum driving” shows how to set a Hamiltonian which drives the dynamics of a system along instantaneous eigenstates of a reference Hamiltonian to reproduce the same final result of an adiabatic process in a shorter time. In this paper, motivated by transitionless quantum driving, we construct shortcuts to adiabatic passage in a three-atom system to create the Greenberger-Horne-Zeilinger states with the help of quantum Zeno dynamics and of non-resonant lasers. The influence of various decoherence processes is discussed by numerical simulation and the result proves that the scheme is fast and robust against decoherence and operational imperfection.
Biogeographical role of the Kuroshio Current in the amphibious mudskipper Periophthalmus modestus indicated by mitochondrial DNA data
Authors: He Lijun , Mukai Takahiko , Hou Chu Ka , Ma Qiang , Zhang Jing
Published: October 2015

Quaternary climatic cycles have influenced marine organisms’ spatial distribution and population dynamics. This study aimed to elucidate the evolutionary influences of contemporary and glacial physical barriers on the population structure, demography and colonization history of the mudskipper (Periophthalmus modestus) based on a mitochondrial gene segment (ND5) from 131 individual fish sampled in the northwestern Pacific Ocean. The current Kuroshio Current and the glacial exposure of the Taiwan Strait appeared to have restricted migration among the South China Sea, coastal East China and Japan. However, genetic homogeneity (Nm>1) also suggested contemporary larval transportation by sea circulation between the East China Sea and the South China Sea or historical dispersal along the glacial exposed shoreline among China, Japan and the Ryukyu Islands. Evolutionary signals of the strengthened East Asian Summer Monsoon in the mid-Pleistocene and regional difference in intertidal primary productions were indicated by a late-Pleistocene population expansion ofP. modestuswith a higher effective population size in the South China Sea than in the East China Sea. Furthermore, a potential colonization origin from the South China Sea was consistently inferred by different clues, including the populations’ coalescence times, the ancestral haplotype distribution, the number of private haplotypes and species/genetic diversity.
Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species
Authors: Kim Kyunghee , Lee Sang-Choon , Lee Junki , Yu Yeisoo , Yang Kiwoung , Choi Beom-Soon , Koh Hee-Jong , Waminal Nomar Espinosa , Choi Hong-Il , Kim Nam-Hoon , Jang Woojong , Park Hyun-Seung , Lee Jonghoon , Lee Hyun Oh , Joh Ho Jun , Lee Hyeon Ju , Park Jee Young , Perumal Sampath , Jayakodi Murukarthick , Lee Yun Sun , Kim Backki , Copetti Dario , Kim Soonok , Kim Sunggil , Lim Ki-Byung , Kim Young-Dong , Lee Jungho , Cho Kwang-Su , Park Beom-Seok , Wing Rod A. , Yang Tae-Jin
Published: October 2015

Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis.
Development of High Resolution Melting Analysis for the Diagnosis of Human Malaria
Authors: Chua Kek Heng , Lim Siew Chee , Ng Ching Ching , Lee Ping Chin , Lim Yvonne Ai Lian , Lau Tze Pheng , Chai Hwa Chia
Published: October 2015

Molecular detection has overcome limitations of microscopic examination by providing greater sensitivity and specificity in Plasmodium species detection. The objective of the present study was to develop a quantitative real-time polymerase chain reaction coupled with high-resolution melting (qRT-PCR-HRM) assay for rapid, accurate and simultaneous detection of all five human Plasmodium spp. A pair of primers targeted the 18S SSU rRNA gene of the Plasmodium spp. was designed for qRT-PCR-HRM assay development. Analytical sensitivity and specificity of the assay were evaluated. Samples collected from 229 malaria suspected patients recruited from Sabah, Malaysia were screened using the assay and results were compared with data obtained using PlasmoNexTM, a hexaplex PCR system. The qRT-PCR-HRM assay was able to detect and discriminate the five Plasmodium spp. with lowest detection limits of 1–100 copy numbers without nonspecific amplifications. The detection of Plasmodium spp. in clinical samples using this assay also achieved 100% concordance with that obtained using PlasmoNexTM. This indicated that the diagnostic sensitivity and specificity of this assay in Plasmodium spp. detection is comparable with those of PlasmoNexTM. The qRT-PCR-HRM assay is simple, produces results in two hours and enables high-throughput screening. Thus, it is an alternative method for rapid and accurate malaria diagnosis.
Effect of the thin-film limit on the measurable optical properties of graphene
Authors: Holovský Jakub , Nicolay Sylvain , De Wolf Stefaan , Ballif Christophe
Published: October 2015

The fundamental sheet conductance of graphene can be directly related to the product of its absorption coefficient, thickness and refractive index. The same can be done for graphene’s fundamental opacity if the so-called thin-film limit is considered. Here, we test mathematically and experimentally the validity of this limit on graphene, as well as on thin metal and semiconductor layers. Notably, within this limit, all measurable properties depend only on the product of the absorption coefficient, thickness and refractive index. As a direct consequence, the absorptance of graphene depends on the refractive indices of the surrounding media. This explains the difficulty in determining separately the optical constants of graphene and their widely varying values found in literature so far. Finally, our results allow an accurate estimation of the potential optical losses or gains when graphene is used for various optoelectronic applications.
Discovery of Small Molecules that Inhibit the Disordered Protein, p27Kip1
Authors: Iconaru Luigi I. , Ban David , Bharatham Kavitha , Ramanathan Arvind , Zhang Weixing , Shelat Anang A. , Zuo Jian , Kriwacki Richard W.
Published: October 2015

Disordered proteins are highly prevalent in biological systems, they control myriad signaling and regulatory processes and their levels and/or cellular localization are often altered in human disease. In contrast to folded proteins, disordered proteins, due to conformational heterogeneity and dynamics, are not considered viable drug targets. We challenged this paradigm by identifying through NMR-based screening small molecules that bound specifically, albeit weakly, to the disordered cell cycle regulator, p27Kip1 (p27). Two groups of molecules bound to sites created by transient clusters of aromatic residues within p27. Conserved chemical features within these two groups of small molecules exhibited complementarity to their binding sites within p27, establishing structure-activity relationships for small molecule:disordered protein interactions. Finally, one compound counteracted the Cdk2/cyclin A inhibitory function of p27 in vitro, providing proof-of-principle that small molecules can inhibit the function of a disordered protein (p27) through sequestration in a conformation incapable of folding and binding to a natural regulatory target (Cdk2/cyclin A).
A competing risk analysis of sequential complication development in Asian type 2 diabetes mellitus patients
Authors: Cheng Li-Jen , Chen Jeng-Huei , Lin Ming-Yen , Chen Li-Chia , Lao Chun-Huan , Luh Hsing , Hwang Shang-Jyh
Published: October 2015

This retrospective cohort study investigated the progression risk of sequential complication in Asian type 2 diabetes (T2D) patients using the Taiwan Pay-for-Performance Diabetes Registry and claim data from November 2003 to February 2009. 226,310 adult T2D patients without complication were followed from diagnosis to complications, including myocardial infarction (MI), other ischemic heart disease (IHD), congestive heart failure (CHF), stroke, chronic kidney disease (CKD), retinopathy, amputation, death or to the end of study. Cumulative incidences (CIs) of first and second complications were analyzed in 30 and 4 years using the cumulative incidence competing risk method. IHD (29.8%), CKD (24.5%) and stroke (16.0%) are the most common first complications. The further development of T2D complications depends on a patient’s existing complication profiles. Patients who initially developed cardiovascular complications had a higher risk (9.2% to 24.4%) of developing IHD or CKD, respectively. All-cause mortality was the most likely consequence for patients with a prior MI (12.0%), so as stroke in patients with a prior MI (10.8%) or IHD (8.9%). Patients with CKD had higher risk of developing IHD (16.3%), stroke (8.9%) and all-cause mortality (8.7%) than end-stage renal disease (4.0%). Following an amputation, patients had a considerable risk of all-cause mortality (42.1%).
Choroidal neovascularization is inhibited via an intraocular decrease of inflammatory cells in mice lacking complement component C3
Authors: Tan Xue , Fujiu Katsuhito , Manabe Ichiro , Nishida Junko , Yamagishi Reiko , Nagai Ryozo , Yanagi Yasuo
Published: October 2015

In early age-related macular degeneration (AMD), complement component C3 can be observed in drusen, which is the accumulation of material beneath the retinal pigment epithelium. The complement pathways, via the activation of C3, can upregulate the expression of cytokines and their receptors and the recruitment of inflammatory leukocytes, both of which play an important role in the development of choroidal neovascularization (CNV) in exudative AMD. Laser-induced CNV lesions were found to be significantly smaller in C3−/− mice than in wild-type mice. By using flow cytometry, we demonstrated that the proportions of intraocular granulocytes, CD11b+F4/80+Ly6Chi and CD11b+F4/80+Ly6Clo cells, were lower in C3−/− mice than in wild-type mice as early as day 1 after laser injury and the proportions of granulocytes and three macrophage/monocyte subsets were significantly lower on day 3. In contrast, C3−/− mice had more granulocytes and CD11b+F4/80+Ly6Chi cells in peripheral blood than wild-type mice after injury. Further, the expression levels of Vegfa164 were upregulated in intraocular Ly6Chi macrophages/monocytes of C3−/− mice, but not as much as in wild-type mice. Collectively, our data demonstrate that despite a more pronounced induction of systemic inflammation, inhibition of complement factor C3 suppresses CNV by decreasing the recruitment of inflammatory cells to the lesion.
The effect of environmental heterogeneity on species richness depends on community position along the environmental gradient
Authors: Yang Zhiyong , Liu Xueqi , Zhou Mohua , Ai Dexiecuo , Wang Gang , Wang Youshi , Chu Chengjin , Lundholm Jeremy T.
Published: October 2015

Environmental heterogeneity is among the most important factors governing community structure. Besides the widespread evidence supporting positive relationships between richness and environmental heterogeneity, negative and unimodal relationships have also been reported. However, few studies have attempted to test the role of the heterogeneity on species richness after removing the confounding effect of resource availability or environmental severity. Here we constructed an individual-based spatially explicit model incorporating a long-recognized tradeoff between competitive ability and stress-tolerance ability of species. We explored the impact of the level of resource availability (i.e. the position of the community along a gradient of environmental severity) on the heterogeneity-diversity relationship (HDR). The results indicate that the shape of HDR depends on the community position along the environmental gradient: at either end of the gradient of environmental severity, a positive HDR occurred, whereas at the intermediate levels of the gradient, a unimodal HDR emerged. Our exploration demonstrates that resource availability/environmental severity should be considered as a potential factor influencing the shape of the HDR. Our theoretical predictions represent hypotheses in need of further empirical study.
Nondestructive detection of lead chrome green in tea by Raman spectroscopy
Authors: Li Xiao-Li , Sun Chan-Jun , Luo Liu-Bin , He Yong
Published: October 2015

Raman spectroscopy was first adopted for rapid detecting a hazardous substance of lead chrome green in tea, which was illegally added to tea to disguise as high-quality. 160 samples of tea infusion with different concentrations of lead chrome green were prepared for Raman spectra acquirement in the range of 2804 cm−1–230 cm−1 and the spectral intensities were calibrated with relative intensity standards. Then wavelet transformation (WT) was adopted to extract information in different time and frequency domains from Raman spectra and the low-frequency approximation signal (ca4) was proved as the most important information for establishment of lead chrome green measurement model and the corresponding partial least squares (PLS) regression model obtained good performance in prediction with Rp and RMSEP of 0.936 and 0.803, respectively. To further explore the important wavenumbers closely related to lead chrome green, successive projections algorithm (SPA) was proposed. Finally, 8 characteristic wavenumbers closely related to lead chrome green were obtained and a more convenient and fast model was also developed. These results proved the feasibility of Raman spectroscopy for nondestructive detection of lead chrome green in tea quality control.
Plasmon-Induced Transparency by Hybridizing Concentric-Twisted Double Split Ring Resonators
Authors: Parvinnezhad Hokmabadi Mohammad , Philip Elizabath , Rivera Elmer , Kung Patrick , Kim Seongsin M.
Published: October 2015

As a classical analogue of electromagnetically induced transparency, plasmon induced transparency (PIT) has attracted great attention by mitigating otherwise cumbersome experimental implementation constraints. Here, through theoretical design, simulation and experimental validation, we present a novel approach to achieve and control PIT by hybridizing two double split ring resonators (DSRRs) on flexible polyimide substrates. In the design, the large rings in the DSRRs are stationary and mirror images of each other, while the small SRRs rotate about their center axes. Counter-directional rotation (twisting) of the small SRRs is shown to lead to resonance shifts, while co-directional rotation results in splitting of the lower frequency resonance and emergence of a PIT window. We develop an equivalent circuit model and introduce a mutual inductance parameter M whose sign is shown to characterize the existence or absence of PIT response from the structure. This model attempts to provide a quantitative measure of the physical mechanisms underlying the observed PIT phenomenon. As such, our findings can support the design of several applications such as optical buffers, delay lines and ultra-sensitive sensors.
Time-averaged serum potassium levels and its fluctuation associate with 5-year survival of peritoneal dialysis patients: two-center based study
Authors: Li Shen-Heng , Xie Jian-Teng , Long Hai-Bo , Zhang Jun , Zhou Wei-Dong , Niu Hong-Xin , Tang Xun , Feng Zhong-Lin , Ye Zhi-Ming , Zuo Yang-Yang , Fu Lei , Wen Feng , Wang Li-Ping , Wang Wen-Jian , Shi Wei
Published: October 2015

The time-averaged serum potassium was more comprehensive to reflect the all-time changes of serum potassium levels during peritoneal dialysis (PD). However, the association of fluctuation of time-averaged serum potassium level with long-time survival of PD patients remains unknown. In this retrospective study, we included 357 incident PD patients in 2 centers from January 1, 2007 to October 31, 2012 with follow-up through October 31, 2014. Our data demonstrated that it was the lower time-averaged serum potassium level rather than baseline of serum potassium level that was associated with high risk of death. Patients with higher standard deviation (SD) had significantly poorer all-cause (p = 0.016) and cardiovascular mortality (p = 0.041). Among the patients with time-averaged serum potassium levels below 4.0 mEq/L, a lower mean value was more important than its SD to predict death risk. In contrast, the patients with time-averaged serum potassium levels above 4.0 mEq/L, those with serum potassium SD < 0.54 mEq/L, exhibited a higher 3-year and 5-year survival rate for both all-cause and cardiovascular mortality compared to the control groups. Our data clearly suggested both time-averaged serum potassium and its fluctuation contributed disproportionately to the high death risk in PD patients.
Dramatic increase in SHP2 binding activity of Helicobacter pylori Western CagA by EPIYA-C duplication: its implications in gastric carcinogenesis
Authors: Nagase Lisa , Hayashi Takeru , Senda Toshiya , Hatakeyama Masanori
Published: October 2015

Infection with cagA-positive Helicobacter pylori is critically associated with the development of gastric cancer. The cagA-encoded CagA is delivered into gastric epithelial cells via type IV secretion, where it interacts with and thereby deregulates the pro-oncogenic phosphatase SHP2. East Asian CagA and Western CagA are two major CagA species produced by H. pylori circulating in East Asian countries and in the rest of the world, respectively. The SHP2 binding site of Western CagA, termed the EPIYA-C segment, variably duplicates and infection with H. pylori carrying Western CagA with multiple EPIYA-C segments is a distinct risk factor of gastric cancer. Here we show that duplication of EPIYA-C from one to two or more increases SHP2 binding of Western CagA by more than one hundredfold. Based on the decisive difference in SHP2 binding, Western CagA can be divided into two types: type I CagA carrying a single EPIYA-C segment and type II CagA carrying multiple EPIYA-C segments. Gastric epithelial cells expressing type II CagA acquire the ability to invade extracellular matrices, a malignant cellular trait associated with deregulated SHP2. A big leap in SHP2 binding activity may therefore provide molecular basis that makes type II Western CagA a distinct gastric cancer risk.
Systemic Risk Analysis on Reconstructed Economic and Financial Networks
Authors: Cimini Giulio , Squartini Tiziano , Garlaschelli Diego , Gabrielli Andrea
Published: October 2015

We address a fundamental problem that is systematically encountered when modeling real-world complex systems of societal relevance: the limitedness of the information available. In the case of economic and financial networks, privacy issues severely limit the information that can be accessed and, as a consequence, the possibility of correctly estimating the resilience of these systems to events such as financial shocks, crises and cascade failures. Here we present an innovative method to reconstruct the structure of such partially-accessible systems, based on the knowledge of intrinsic node-specific properties and of the number of connections of only a limited subset of nodes. This information is used to calibrate an inference procedure based on fundamental concepts derived from statistical physics, which allows to generate ensembles of directed weighted networks intended to represent the real system—so that the real network properties can be estimated as their average values within the ensemble. We test the method both on synthetic and empirical networks, focusing on the properties that are commonly used to measure systemic risk. Indeed, the method shows a remarkable robustness with respect to the limitedness of the information available, thus representing a valuable tool for gaining insights on privacy-protected economic and financial systems.
Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut
Authors: Milani Christian , Lugli Gabriele Andrea , Duranti Sabrina , Turroni Francesca , Mancabelli Leonardo , Ferrario Chiara , Mangifesta Marta , Hevia Arancha , Viappiani Alice , Scholz Matthias , Arioli Stefania , Sanchez Borja , Lane Jonathan , Ward Doyle V. , Hickey Rita , Mora Diego , Segata Nicola , Margolles Abelardo , van Sinderen Douwe , Ventura Marco
Published: October 2015

Bifidobacteria are common and frequently dominant members of the gut microbiota of many animals, including mammals and insects. Carbohydrates are considered key carbon sources for the gut microbiota, imposing strong selective pressure on the complex microbial consortium of the gut. Despite its importance, the genetic traits that facilitate carbohydrate utilization by gut microbiota members are still poorly characterized. Here, genome analyses of 47 representative Bifidobacterium (sub)species revealed the genes predicted to be required for the degradation and internalization of a wide range of carbohydrates, outnumbering those found in many other gut microbiota members. The glycan-degrading abilities of bifidobacteria are believed to reflect available carbon sources in the mammalian gut. Furthermore, transcriptome profiling of bifidobacterial genomes supported the involvement of various chromosomal loci in glycan metabolism. The widespread occurrence of bifidobacterial saccharolytic features is in line with metagenomic and metatranscriptomic datasets obtained from human adult/infant faecal samples, thereby supporting the notion that bifidobacteria expand the human glycobiome. This study also underscores the hypothesis of saccharidic resource sharing among bifidobacteria through species-specific metabolic specialization and cross feeding, thereby forging trophic relationships between members of the gut microbiota.
Messenger RNA-based therapeutics for the treatment of apoptosis-associated diseases
Authors: Matsui Akitsugu , Uchida Satoshi , Ishii Takehiko , Itaka Keiji , Kataoka Kazunori
Published: October 2015

Gene therapy is a promising approach for treating diseases that are closely associated with excessive apoptosis, because the gene can effectively and sustainably introduce anti-apoptotic factors into cells. However, DNA delivery poses the risk of random genomic integration, leading to overexpression of the delivered gene and cancer development. Messenger RNA (mRNA) can evade integration events in target cells. We examined the use of mRNA-based therapeutics for introducing anti-apoptotic factors by using a mouse model of fulminant hepatitis. For introducing mRNA into the liver, a synthesised polymer-based carrier of polyplex nanomicelles was used for hydrodynamic intravenous injection. Using GFP as a reporter, we demonstrate that mRNA delivery induced efficient protein expression in almost 100% of liver cells, while plasmid DNA (pDNA) delivery provided a smaller percentage of GFP-positive cells. Analyses using Cy5-labelled mRNA and pDNA revealed that efficient expression by mRNA was attributed to a simple intracellular mechanism, without the need for nuclear entry. Consistent with this observation, Bcl-2 mRNA was more effective on reducing apoptosis in the liver of mice with fulminant hepatitis than Bcl-2 pDNA. Therefore, mRNA-based therapeutics combined with an effective delivery system such as polyplex nanomicelles is a promising treatment for intractable diseases associated with excessive apoptosis.
Inferring Infection Patterns Based on a Connectivity Map of Host Transcriptional Responses
Authors: Han Lu , He Haochen , Li Fei , Cui Xiuliang , Xie Dafei , Liu Yang , Zheng Xiaofei , Bai Hui , Wang Shengqi , Bo Xiaochen
Published: October 2015

Host responses to infections represent an important pathogenicity determiner and delineation of host responses can elucidate pathogenesis processes and inform the development of anti-infection therapies. Low cost, high throughput, easy quantitation and rich descriptions have made gene expression profiling generated by DNA microarrays an optimal approach for describing host transcriptional responses (HTRs). However, efforts to characterize the landscape of HTRs to diverse pathogens are far from offering a comprehensive view. Here, we developed an HTR Connectivity Map based on systematic assessment of pairwise similarities of HTRs to 50 clinically important human pathogens using 1353 gene-expression profiles generated from >60 human cells/tissues. These 50 pathogens were further partitioned into eight robust “HTR communities” (i.e., groups with more consensus internal HTR similarities). These communities showed enrichment in specific infection attributes and differential gene expression patterns. Using query signatures of HTRs to external pathogens, we demonstrated four distinct modes of HTR associations among different pathogens types/class and validated the reliability of the HTR community divisions for differentiating and categorizing pathogens from a host-oriented perspective. These findings provide a first-generation HTR Connectivity Map of 50 diverse pathogens and demonstrate the potential for using annotated HTR community to detect functional associations among infectious pathogens.
QTL mapping of cucumber fruit flesh thickness by SLAF-seq
Authors: Xu Xuewen , Lu Lu , Zhu Biyun , Xu Qiang , Qi Xiaohua , Chen Xuehao
Published: October 2015

Cucumber is an agriculturally and economically important vegetable crop worldwide. Fruit flesh thickness is an important trait for cucumber and also a central determinant of yield, yet little is known about the underlying mechanism of this trait. In this study, bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) was applied to finely map the gene that underlies fruit flesh thickness in cucumber. A 0.19-Mb-long quantitative trait locus on chromosome 2 controlling fruit flesh thickness (QTL fft2.1) was identified and further confirmed by simple sequence repeat (SSR) marker-based classical QTL mapping in 138 F2 individuals. Gene prediction of this 0.19-Mb region identified 20 genes. Quantitative RT-PCR revealed higher expression levels of Csa2 M058670.1 (SET domain protein-lysine methyltransferase) in D8 (thick fruit flesh parent) compared with that in XUE1 (thin fruit flesh parent) during fruit development. Sequence alignment analysis of Csa2M058670.1 from thick and thin fruit flesh cucumber lines revealed a 4-bp deletion mutation in the promoter region of this candidate gene, which may result in the loss of Csa2M058670.1 activation in thin fruit flesh lines. The data presented herein suggest that Csa2M058670.1 is a possible candidate gene for controlling flesh thickness in cucumber.