bluuebunny/crossref_metadata_2025 huggingface dataset:
GMM ESTIMATION AND UNIFORM SUBVECTOR INFERENCE WITH POSSIBLE IDENTIFICATION FAILURE
Authors: Andrews Donald W.K. , Cheng Xu
Published: November 2013

This paper determines the properties of standard generalized method of moments (GMM) estimators, tests, and confidence sets (CSs) in moment condition models in which some parameters are unidentified or weakly identified in part of the parameter space. The asymptotic distributions of GMM estimators are established under a full range of drifting sequences of true parameters and distributions. The asymptotic sizes (in a uniform sense) of standard GMM tests and CSs are established.

The paper also establishes the correct asymptotic sizes of “robust” GMM-based Wald,t, and quasi-likelihood ratio tests and CSs whose critical values are designed to yield robustness to identification problems.

The results of the paper are applied to a nonlinear regression model with endogeneity and a probit model with endogeneity and possibly weak instrumental variables.
Multilingual Education Policy in South Africa Constrained by Theoretical and Historical Disconnections
Authors: Heugh Kathleen
Published: November 2013

Multilingual education policy has been a controversial affair in South Africa, especially over the last 60 years. Recent research conducted by government-led and independent agencies shows declining student achievement within an education system that employs 11 home languages for education in the first three grades of primary school, followed by a transition to English medium for the majority (approximately 80%) of speakers of African languages. Research that focuses on the linguistic practices of students in urban settings suggests that there is a disjuncture between the construction of multilingualism within contemporary education policy and the multilingual reality of students (e.g., Heugh, 2003; Makoni, 2003; Makoni & Pennycook, 2012; Plüddemann, 2013; Probyn, 2009; Stroud & Heugh, 2011). There is also a disjunction between constitutional and other government policies that advance, on paper, a multilingual policy, yet are implemented through an assimilatory drive towards English (Alexander & Heugh, 1999). As predicted nearly two decades ago, the ideological framing of multilingualism during the negotiations in the early 1990s was to have consequences for the way in which language policy would unfold in the education sector over the next 20 to 30 years (Heugh, 1995, 1999). While poor student achievement in school may be ascribed to a range of socioeconomic indicators, this article draws attention to contributory factors that relate to language(s) in education. These include different constructions of multilingualism in education in relation to sociolinguistic and educational linguistic considerations, contradictory interpretations of multilingual education in a series of education policy documents, pedagogical weaknesses, and recent attempts to strengthen the provision of African languages education alongside English in the first 10 years of school (Grades R and 0–9; e.g., Department of Basic Education (DBE), 2013a, 2013b).
Fertilization capacity of cryopreserved Iberian ibex epididymal sperm in a heterologousin vitrofertilization assay
Authors: López-Saucedo J. , Santiago-Moreno J. , Fierro R. , Izquierdo D. , Coloma M.A. , Catalá M.G. , Jiménez I. , Paramio M.T.
Published: November 2013

In vitrofertilization (IVF) can be used to assess the fertilization capacity of sperm. Heterologous IVF may be useful when assessing that of wild animals as it is often difficult to obtain adequate numbers of naturally corresponding oocytes. The aim of the present study was to assess the fertilization capacity of frozen–thawed ibex epididymal spermatozoa via heterologous IVF involving the oocytes of prepubertal domestic goats. The effect on fertilization and embryo development of adding oestrous sheep serum (ESS) to the fertilization medium was also examined. Cumulus–oocyte complexes (COCs) were matured in TCM-199 for 24–27 h at 38.5°C in a 5% CO2in air atmosphere. Frozen–thawed epididymal spermatozoa were selected by density gradient centrifugation. After maturation, the oocytes were co-incubated with spermatozoa in synthetic oviductal fluid (SOF) with different concentrations of ESS: SOF-C (0%), SOF-2 (2%) and SOF-20 (20%). At 17 h post-insemination (hpi), zygotes with one female and one male pronucleus (2PN) were categorised as normal; zygotes with 3PN were recorded as polyspermic, and oocytes with 1PN as asynchronous. Cleavage and blastocyst development were assessed at 48 and 168 hpi respectively. The percentage of zygotes with 2PN was higher in the SOF-2 than in the SOF-20 treatment group (27.7% versus 2.9%P< 0.05). The percentage of blastocysts formed with the SOF-C, SOF-2 and SOF-20 treatments were 1.1%, 7.5% and 0% respectively. These results show that the presence of 2% ESS achieves better results than the use of no serum or the standard 20% concentration. Heterologous IVF may be an effective method for predicting the fertilization capacity of ibex spermatozoa, and therefore perhaps that of other wild mountain ungulates.
From Cradle of European Civilization to Grave Austerity: Does Greece Face a Creeping Health Disaster?
Authors: Levett Jeffrey
Published: November 2013

LevettJ.From cradle of European civilization to grave austerity: does Greece face a creeping health disaster?Prehosp Disaster Med.2013;28(6):1-2.

While the global financial crisis started on the American continent, Greece has felt the biggest shock. As a result of government-imposed austerity measures following the implementation of the Memorandum of Understanding,* population health and the health sector have been impacted. This adds a burden to the national health system (NHS), already facing compromised efficiency and effectiveness. Cuts in health and social protection budgets are an additional exacerbation. These events have precipitated serious discussion, variable opinions, and related activity, but there is limited research on the public health impact of austerity.1In 2011, I suggested that the Memorandum could be damaging to health and that there is a creeping health disaster2while Kentikelenis referred to the omens of disaster.3If austerity was tested like a medication in a clinical trial, it would have been stopped long ago, given its deadly side effects, according to Stuckler and Basu.4According to Blyth, austerity is a dangerous idea.5In terms of the Utstein template,6–8austerity is designated a health hazard, which can be exacerbated when national governance is weak.9The outcome is a creeping disaster of uncertain dynamics.†
Phylogenetic patterns of character evolution in the hyobranchial apparatus of early tetrapods
Authors: Witzmann Florian
Published: November 2013

The morphologies of the hyobranchial apparatus in early tetrapods are reviewed, based primarily on first-hand examination and supplemented by published descriptions. The basic arrangement of the “aquatic” hyobranchium, with four pairs of branchial arches and internal gills, was conserved to a remarkable degree across the fish–to–tetrapod transition and was retained in further evolution in adults of several tetrapod lineages. Thus, a fish-like hyobranchium in basal tetrapods does not necessarily represent a larval or paedomorphic character, respectively, as was often suggested in analogy to extant salamanders. Rather, it represents the plesiomorphic state of the adult hyobranchium in tetrapods. The changes in the hyobranchium during the fish–to–tetrapod transition include the reduction of the number of skeletal elements and their morphological simplification. In all three presently discussed scenarios of lissamphibian origin, the temnospondyl, lepospondyl and diphyly hypotheses, the internal gills were reduced independently within temnospondyls and on the amniote stem below seymouriamorphs. Evidence of remodelling into a true “terrestrial” hyobranchium, with reduction of the posterior branchial arches and modification to support terrestrial tongue feeding, is scarce in early tetrapods. It evolved within temnospondyls in zatracheids, amphibamids and lissamphibians, as well as once or several times in early amniotes or in their immediate stem-forms.
Implications of Current Developments in International Liability for the Practice of Marine Geo-engineering Activities
Authors: KIM Jung-Eun
Published: November 2013

Ocean fertilization was first introduced as a carbon dioxide mitigation technique in the 1980s. However, its effectiveness to slow down climate change is uncertain and it is expected to damage the marine environment. Consequently, international law, including the London Convention/Protocol and the Convention on Biological Diversity, limits this activity to scientific research purposes. The applicability and scope of existing treaties for regulating this activity have been reviewed within international legal systems, in particular within the London Protocol. The establishment of a liability regime with respect to these activities has also been raised during a discussion on regulation of ocean fertilization under the London Protocol. One of the key purposes of the liability regime could be to make ocean users more cautious when exploring and exploiting the oceans through charging cleaning costs or imposing compensation for damage. This paper aims to identify such a preventative effect of the international liability regime, in particular, state liability.
Legal Effect of Maps in Maritime Boundary Delimitation: A Response to Erik Franckx and Marco Benatar
Authors: ZHENG Zhihua
Published: November 2013

The Chinese traditional maritime boundary line (U-line) in the South China Sea (SCS) and its validity under international law have been challenged by bordering states and some scholars. In 2012, Franckx and Benatar questioned the validity of the U-line in view of factors such as the intent of the state reflected by the map, the cartographer's neutrality, technical accuracy, consistency of the cartographic material, and recognition and acquiescence by the international community. This paper points out that the SCS U-line drawn by the Chinese government in 1947, at the median position between China's SCS islands and reefs, and the coastlines of bordering states, reflects the scope of China's claims and intent. The consistency of the claims has been maintained by the PRC after 1949, and the claims have been recognised or acquiesced to by bordering states over quite a long period. Therefore, the U-line has probative force under international law.
Probing the atomic structure of metallic nanoclusters with the tip of a scanning tunneling microscope
Authors: Schouteden Koen , Lauwaet Koen , Janssens Ewald , Barcaro Giovanni , Fortunelli Alessandro , Van Haesendonck Chris , Lievens Peter
Published: November 2013

Visualization of the three-dimensional atomic structure of deposited Co clusters is demonstrated by scanning tunneling microscopy using a functionalized tip.
Rapid synthesis of highly luminescent and stable Au20 nanoclusters for active tumor-targeted imaging in vitro and in vivo
Authors: Zhang Pu , Yang Xiao Xi , Wang Yi , Zhao Ning Wei , Xiong Zu Hong , Huang Cheng Zhi
Published: November 2013

Receptor-mediated uptake of nanoprobes for tumor-targeting in vitro and in vivo is systematically studied using newly prepared luminescent Au20 nanoclusters.
The role of protein characteristics in the formation and fluorescence of Au nanoclusters
Authors: Xu Yaolin , Sherwood Jennifer , Qin Ying , Crowley Dorothy , Bonizzoni Marco , Bao Yuping
Published: November 2013

The size and composition of the protein templates are critically important to the formation, fluorescence, and stability of Au nanoclusters.
Synthesis and in vitro evaluation of tetrahydroisoquinolines with pendent aromatics as sigma-2 (σ2) selective ligands
Authors: Ashford Mark E. , Nguyen Vu H. , Greguric Ivan , Pham Tien Q. , Keller Paul A. , Katsifis Andrew
Published: November 2013

Sigma-2 selective ligands – a SAR study showing increased potency and selectivity with derivatives showing the potential to be converted into radiolabelled ligands.
High electrocatalytic activity of low-loaded transparent carbon nanotube assemblies for CoII/III-mediated dye-sensitized solar cells
Authors: Seo Seon Hee , Kim Mi Hyung , Jeong Eun Ji , Yoon Sung Hwan , Kang Hyon Chol , Cha Seung I. , Lee Dong Yoon
Published: November 2013

High optoelectrochemical and photovoltaic performances were achieved for CoII/III-mediated DSCs using a carbon nanotube electrocatalyst with a loading of <5 μg cm−2.
Hybrid porous polymers constructed from octavinylsilsesquioxane and benzene via Friedel–Crafts reaction: tunable porosity, gas sorption, and postfunctionalization
Authors: Wu Yue , Wang Dengxu , Li Liguo , Yang Wenyan , Feng Shengyu , Liu Hongzhi
Published: November 2013

Based on the multi-reaction sites of benzene in the Friedel–Crafts reaction with octavinylsilsesquioxane, hybrid polymers with tunable porosity were prepared.
General and efficient outage evaluation approach of asymmetric two‐way AF relaying
Authors: Shi Jingjing , Ge Jianhua , Li Jing , Gao Yang , Zhang Nan
Published: November 2013

An effective outage evaluation approach of asymmetric two‐way amplify‐and‐forward relaying is presented. The proposed approach, characterised by generality, can be applicable to various realistic fading channels. The analytical and simulation results in Nakagami‐m fading demonstrate the accuracy of the approach.
U‐band 3D integrated bandpass filter with four controllable transmission zeros
Authors: Zhang Gang , Wang Jianpeng , Xu Xin
Published: November 2013

A three‐dimensional integrated substrate integrated waveguide bandpass filter has been demonstrated by using low‐temperature co‐fired ceramic technology. By adopting the extracted‐pole and the cross‐coupling mechanisms simultaneously, four controllable finite transmission zeros outside the passband are achieved to realise high selectivity. A U‐band prototype has been designed, fabricated and tested. The measured results match well with the predicted theoretical counterparts. The proposed filter has the merits of desirable insertion loss, high design freedom and good out‐of‐band rejection.
Modular inversion based on digit‐level speculative addition
Authors: Cilardo A.
Published: November 2013

A solution for the computation of modular inversion based on speculative addition is presented. The proposed circuit effectively addresses the problem of long carry chains caused by signed operations and allows fast low‐overhead implementations of modular inversion. The solution is particularly suitable for devices providing optimised carry‐propagation logic such as field‐programmable gate arrays.
Genetic‐based design of a tetra‐band high‐efficiency radio‐frequency energy harvesting system
Authors: Masotti Diego , Costanzo Alessandra , Del Prete Massimo , Rizzoli Vittorio
Published: November 2013

In this study, we exploit genetic algorithms to design a rectenna required to harvest ambient radio‐frequency (RF) energy from four different RF bands in critical (ultra‐low power) conditions. For this purpose a set of multi‐resonant annular‐ring patch antennas are pixel‐wise described inside an electromagnetic simulator to provide the ‘population’ of individuals among which the genetic tool is able to select the most adapted one with respect to the design specifications. The further use of circuit‐level non‐linear simulation tool, based on Harmonic balance technique, allows the rigorous multi‐band design of the whole rectenna system in RF stationary conditions at several received power levels. The result is a novel compact, lightweight and highly efficient tetra‐band rectenna, able to harvest RF energy from GSM 900, GSM 1800, UMTS and WiFi sources available in the ambient. At these frequency bands high radiation efficiency is desired as an essential prerequisite for optimally handling very low‐power densities. Very good agreement with measurements of both the radiating and rectifying designs is demonstrated in real office scenarios. Finally the rectenna is connected to a power management unit and the resulting assembly is tested in terms of stored energy while harvesting from a mobile cell‐phone call.
Low‐phase noise oscillator utilising high‐Q active resonator based on substrate integrated waveguide technique
Authors: Chen Zhe , Hong Wei , Chen Ji Xin , Zhou Jianyi , Li Lin Sheng
Published: November 2013

An X‐band low‐phase noise planar oscillator employing the substrate integrated waveguide (SIW) active resonator is demonstrated. By compensating the losses in the SIW cavity with an active feedback loop, the Q‐factor of the SIW active resonator is greatly improved. The measured results show a loaded Q‐factor of 1569 and unloaded Q‐factor of 8782, which is very high among other planar resonators. A simplified generalised phase noise condition and its optimisation approach are proposed for the low‐phase noise oscillator design. To validate the proposed optimisation approach, experimental prototypes of oscillators using different design parameters and resonators are fabricated. The measured results show that the optimised SIW active resonator oscillator possesses low‐phase noise of −109.2 dBc/Hz at 100 kHz at X‐band, which is 17 and 9 dB better than the microstrip resonator oscillator and SIW passive resonator oscillator, and is comparable with the dielectric resonator oscillator measured in this study.
Electrochemical activation of substrate surfaces in microelectroforming
Authors: Shao Ligeng , Du Liqun , Wang Liding
Published: November 2013

Microelectroforming is a modern manufacturing process for producing metal microstructures in the field of microelectronic mechanical systems. Electrochemical activation of the substrate surfaces can enhance the adhesion strength between the electroforming layer and the substrate at the first stage of microelectroforming. The mechanism of current density affecting the activation of the substrate surfaces was explored. The cathodic overpotential was carried out with the chronopotentiometric method under different current density conditions. The current density at the first stage of microelectroforming was the largest contributor to the electrochemical activation of the substrate surfaces. As the current density was set in the range of 0.2–1.2 A/dm2, effective electrochemical activation occurred on the substrate surfaces. Although the current density was 0.4 A/dm2, the effect of substrate activation is optimal and the adhesion strength between the electroforming layer and the substrate reached its maximum.
HIV service capacity: identifying current and future areas of clinical shortage
Authors: Mallitt Kylie-Ann , Jansson James , Wand Handan , Crooks Levinia , Wilson David P.
Published: November 2013

Background The capacity of HIV services to meet the clinical needs of people living with HIV (PLHIV) has not been evaluated. Similarly, whether HIV services are positioned to respond to increases in patient demand outside metropolitan centres over the next decade is unknown. Methods: A novel statistical methodology was used to estimate HIV clinical service capacity in Australia. A survey of HIV services was conducted. Geostatistical analysis was used to identify significant regions of clinical service undersupply relative to the estimated number of PLHIV in 2010 and 2020. Results: In 2010, an estimated 2074 PLHIV (9.7% of all PLHIV) resided in regions more than 15 km from a clinical service provider; 485 PLHIV (2.3% of all PLHIV) live >50 km away. By 2020, this is estimated to rise to 3419 and 807 (11.5% and 2.7% of estimated PLHIV) for 15 km and 50 km, respectively. To meet this demand, the establishment of new HIV services are required in the areas of greatest HIV clinical undersupply. In 2010, these are northern Sydney and western New South Wales, the Queensland mid-north coast and the outer suburbs of Melbourne. At the current estimated rate of increase in PLHIV, areas that will become critically undersupplied by 2020 include south-west Sydney, the outer suburbs of Brisbane and Western Australia. Conclusions: This study provides a quantitative assessment using modern statistical techniques to identify HIV clinical service gaps that is applicable in developed and nondeveloped settings. Training of new HIV clinicians should be directed towards undersupplied areas.
Food security, climate change and genetic resources.
Authors: Zeigler R. S.
Published: November 2013

This chapter provides an overview on food security today, how problems of food production will be exacerbated by climate change, and how, in the case of one crop (rice), access to and use of genetic resources have already begun to address many of the challenges that climate change will bring.
Regional impacts of climate change on agriculture and the role of adaptation.
Authors: Berry P. , Ramirez-Villegas J. , Bramley H. , Mgonja M. A. , Samarendu Mohanty Samarendu Mohanty
Published: November 2013

This chapter discusses the impacts of climate change on agriculture and the role of adaptation. Specifically, the chapter explores the following impacts of climate change on agriculture: increased CO2 concentrations, water availability, and pests and diseases. The chapter also includes reports of case studies on climate change impacts on wheat, rice and millet.
Harnessing meiotic recombination for improved crop varieties.
Authors: Armstrong S. J.
Published: November 2013

This chapter describes how a deeper understanding of sexual reproduction in plants, specifically the processes of meiosis, should lead to better use of germplasm in crop breeding as a response to climate change. It explains why meiotic recombination lies at the heart of generating novel varieties. Knowledge from Arabidopsis thaliana will be implemented and assessed by experiments aimed at altering meiotic recombination in crop species, initially using the closely related brassicas and the cereal crop barley, with the overall aim of providing the plant breeder with the knowledge to modify recombination and potentially develop new varieties.
High temperature stress.
Authors: Djanaguiraman M. , Prasad P. V. V.
Published: November 2013

This chapter discusses the impact of high temperature stress on crops and their wild relatives as well as on species fitness, physiological, growth and yield processes. It describes the role of crop wild relatives and landraces for high temperature stress tolerance, and the traits used in breeding for high temperature stress. Approaches for developing high temperature stress-tolerant genotypes are presented, which include traditional backcross, quantitative trait loci and transgenic approaches.
Drought.
Authors: Ceccarelli S.
Published: November 2013

This chapter discusses the genetics of drought resistance and illustrates examples of the importance of landraces and wild relatives in breeding for drought resistance. The two sources of novel genetic variation are briefly described, i.e. the gene banks and/or the farmers' fields.
Response to flooding: submergence tolerance in rice.
Authors: Ismail A. M. , Mackill D. J.
Published: November 2013

This chapter discusses submergence tolerance as a response to flooding, focusing on rice as a model crop where progress was made in developing flood-tolerant varieties and where opportunities exist for further improvements through mining the enormous genetic diversity available in preserved collections worldwide. The impacts of climate change on rice in flood-prone areas are briefly described. The progress made in exploiting the genetic variation in flooding tolerance-associated traits is summarized for rice germplasm improvement to develop high yielding varieties for flood-affected areas and for areas where floods are expected to worsen with climate change. Future directions in flood tolerance research in rice to cope with climate change are also mentioned.
Effects of climate change on plant-insect interactions and prospects for resistance breeding using genetic resources.
Authors: Pritchard J. , Broekgaarden C. , Vosman B.
Published: November 2013

This chapter describes the components (elevated CO2, temperature and drought) of climate change and their direct and indirect effects on plant-insect interactions. The genetic resources (such as wild relatives and traditional, locally adapted landraces) important for increasing pest/disease resistance in crop plants are described. Some strategies for introduction of pest and disease resistance are presented, which include traditional and biotechnological (genetic modification) approaches.
Does Everything Happen when you are Young? Introducing the Youth Bias
Authors: Koppel Jonathan , Berntsen Dorthe
Published: November 2013

The reminiscence bump refers to the disproportionate number of individuals’ autobiographical memories that date from young adulthood. A similar bump is found in cultural life scripts: When people are asked to nominate and date major transitional events in a typical life course in their culture, a disproportionate number of the events cited are likewise expected to occur in young adulthood. Across two online studies, we tested whether these effects reflect a broader tendency to ascribe most important events to young adulthood. Specifically, we probed, in adult USA samples, for when individuals expect the most important public event of a typical person's life to take place. Although the occurrence of such public events should be randomly distributed across the lifespan, we found a bump in young adulthood. We found this bump in both subjective (Study 1; probing cultural expectations for the expected timing of the public event that a typical person considers to be the most important of their lifetime) and objective (Study 2; probing cultural expectations for the expected timing of the objectively most important public event of a typical person's lifetime) conditions. We term this set of cultural expectations the youth bias and discuss its implications for human cognition.
Agricultural Prices, Selection, and the Evolution of the Food Industry
Authors: Gaigné Carl , Le Mener Léo
Published: November 2013

We present a model that explains the relationship between low input prices, high exit rates, and industrial concentration. We argue that falling input prices force less productive firms to exit the market, and lead to the expansion of more efficient incumbents at the expense of less productive producers. Our model helps reconcile some well‐established empirical results regarding the food processing industry. Indeed, agricultural prices fell between the early 1900s and 2006, and over the same period there was a trend towards higher concentration in the food industry, with an increase in average productivity.
The Impact of Immigration Enforcement on the U.S. Farming Sector
Authors: Kostandini Genti , Mykerezi Elton , Escalante Cesar
Published: November 2013

We examine the effects of local immigration enforcement efforts on U.S. agriculture in dozens of U.S. counties from 2002–2010 by using variations in the timing of adoption of 287(g) programs, which permit local police to enforce immigration law. Difference‐in‐differences models using microdata from the American Community Survey (2005–2010 waves) and county tabulations from the Census of Agriculture (1997, 2002, and 2007) yield robust evidence that county enforcement efforts have reduced immigrant presence in adopting jurisdictions. We also find evidence that wages of farm workers, patterns of farm labor use, output choices, and farm profitability may have been affected in a manner consistent with farm labor shortages.
Temporal changes in the phytoplankton community along the French coast of the eastern English Channel and the southern Bight of the North Sea
Authors: Hernández-Fariñas Tania , Soudant Dominique , Barillé Laurent , Belin Catherine , Lefebvre Alain , Bacher Cédric
Published: November 2013

Long-term trends in the phytoplankton community along the French coast of the English Channel and southern Bight of the North Sea were studied and related to physico-chemical factors and large-climatic indices. Phytoplankton and hydrological data were acquired through three transects. Sampling took place between 1992 and 2011 as part of the French Phytoplankton Monitoring Network (REPHY) and the Regional Nutrients Monitoring Network (SRN). Trends in time-series were identified with dynamic linear models tailored to environmental monitoring data characteristics (e.g. irregular sampling frequency, missing data). Temporal and spatial patterns in the phytoplankton community were explained with a partial triadic analysis. Relationships between the phytoplankton community composition, environmental factors, and climatic indices were assessed using a redundancy analysis (RDA). The analyses revealed long-term changes in the community composition, characterized by a temporal structure that remained common to all transects. The abundance of some groups of taxa such as the one composed by Gymnodinium and Gyrodinium, as well as the group of Pseudo-nitzschia increased during the study period, whereas the abundance of other taxa as for example Guinardia and the group of Coscinodiscus and Stellarima globally decreased. More generally, the proportion of dinoflagellates relative to diatoms increased. Trends in environmental variables were also observed in most sites and related to decreases in nutrient concentrations and an increasing trend in salinity. The RDA indicated that the Atlantic Multidecadal Oscillation index and salinity were the main factors defining the temporal structure of the phytoplankton community. This suggests that variations observed in the phytoplankton community are linked to hydro-climatic changes in the coastal environment.
TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres
Authors: Lin Jiangguo , Countryman Preston , Buncher Noah , Kaur Parminder , E Longjiang , Zhang Yiyun , Gibson Greg , You Changjiang , Watkins Simon C. , Piehler Jacob , Opresko Patricia L. , Kad Neil M. , Wang Hong
Published: November 2013

Human telomeres are maintained by the shelterin protein complex in which TRF1 and TRF2 bind directly to duplex telomeric DNA. How these proteins find telomeric sequences among a genome of billions of base pairs and how they find protein partners to form the shelterin complex remains uncertain. Using single-molecule fluorescence imaging of quantum dot-labeled TRF1 and TRF2, we study how these proteins locate TTAGGG repeats on DNA tightropes. By virtue of its basic domain TRF2 performs an extensive 1D search on nontelomeric DNA, whereas TRF1’s 1D search is limited. Unlike the stable and static associations observed for other proteins at specific binding sites, TRF proteins possess reduced binding stability marked by transient binding (∼9–17 s) and slow 1D diffusion on specific telomeric regions. These slow diffusion constants yield activation energy barriers to sliding ∼2.8–3.6 κBT greater than those for nontelomeric DNA. We propose that the TRF proteins use 1D sliding to find protein partners and assemble the shelterin complex, which in turn stabilizes the interaction with specific telomeric DNA. This ‘tag-team proofreading’ represents a more general mechanism to ensure a specific set of proteins interact with each other on long repetitive specific DNA sequences without requiring external energy sources.
Back to translation: removal of aIF2 from the 5′-end of mRNAs by translation recovery factor in the crenarchaeon Sulfolobus solfataricus
Authors: Märtens Birgit , Manoharadas Salim , Hasenöhrl David , Zeichen Lukas , Bläsi Udo
Published: November 2013

The translation initiation factor aIF2 of the crenarchaeon Sulfolobus solfataricus (Sso) recruits initiator tRNA to the ribosome and stabilizes mRNAs by binding via the γ-subunit to their 5′-triphosphate end. It has been hypothesized that the latter occurs predominantly during unfavorable growth conditions, and that aIF2 or aIF2-γ is released on relief of nutrient stress to enable in particular anew translation of leaderless mRNAs. As leaderless mRNAs are prevalent in Sso and aIF2-γ bound to the 5′-end of a leaderless RNA inhibited ribosome binding in vitro, we aimed at elucidating the mechanism underlying aIF2/aIF2-γ recycling from mRNAs. We have identified a protein termed Trf (translation recovery factor) that co-purified with trimeric aIF2 during outgrowth of cells from prolonged stationary phase. Subsequent in vitro studies revealed that Trf triggers the release of trimeric aIF2 from RNA, and that Trf directly interacts with the aIF2-γ subunit. The importance of Trf is further underscored by an impaired protein synthesis during outgrowth from stationary phase in a Sso trf deletion mutant.
Highly specific and sensitive method for measuring nucleotide excision repair kinetics of ultraviolet photoproducts in human cells
Authors: Choi Jun-Hyuk , Gaddameedhi Shobhan , Kim So-Young , Hu Jinchuan , Kemp Michael G. , Sancar Aziz
Published: November 2013

The nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ∼30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo, we developed a convenient non-radioisotopic method to directly detect DNA excision repair events in human cells. The approach involves extraction of oligonucleotides from UV-irradiated cells, DNA end-labeling with biotin and streptavidin-mediated chemiluminescent detection of the excised UV photoproduct-containing oligonucleotides that are released from the genome during excision repair. Our novel approach is robust, with essentially no signal in the absence of UV or a functional excision repair system. Furthermore, our non-radioisotopic methodology allows for the sensitive detection of excision products within minutes following UV irradiation and does not require additional enrichment steps such as immunoprecipitation. Finally, this technique allows for quantitative measurements of excision repair in human cells. We suggest that the new techniques presented here will be a useful and powerful approach for studying the mechanism of human nucleotide excision repair in vivo.
Discrimination between thermodynamic models ofcis-regulation using transcription factor occupancy data
Authors: Zeigler Robert D. , Cohen Barak A.
Published: November 2013

Many studies have identified binding preferences for transcription factors (TFs), but few have yielded predictive models of how combinations of transcription factor binding sites generate specific levels of gene expression. Synthetic promoters have emerged as powerful tools for generating quantitative data to parameterize models of combinatorial cis-regulation. We sought to improve the accuracy of such models by quantifying the occupancy of TFs on synthetic promoters in vivo and incorporating these data into statistical thermodynamic models of cis-regulation. Using chromatin immunoprecipitation-seq, we measured the occupancy of Gcn4 and Cbf1 in synthetic promoter libraries composed of binding sites for Gcn4, Cbf1, Met31/Met32 and Nrg1. We measured the occupancy of these two TFs and the expression levels of all promoters in two growth conditions. Models parameterized using only expression data predicted expression but failed to identify several interactions between TFs. In contrast, models parameterized with occupancy and expression data predicted expression data, and also revealed Gcn4 self-cooperativity and a negative interaction between Gcn4 and Nrg1. Occupancy data also allowed us to distinguish between competing regulatory mechanisms for the factor Gcn4. Our framework for combining occupancy and expression data produces predictive models that better reflect the mechanisms underlying combinatorial cis-regulation of gene expression.
Spread of epidemic Clostridium difficile NAP1/027 in Latin America: case reports in Panama
Authors: López-Ureña Diana , Quesada-Gómez Carlos , Miranda Erick , Fonseca Mercedes , Rodríguez-Cavallini Evelyn
Published: November 2013

The rate and severity of Clostridium difficile infection (CDI) have been linked to the emergence and spread of the hypervirulent toxigenic strain NAP1/027. This strain has been responsible for large outbreaks in healthcare facilities in North America and Europe and most recently in Latin America. This is the first report of the NAP1 strain in Panama. It suggests that the spread of C. difficile NAP1 throughout Latin America could be a possibility as evidenced in the following case reports. Five isolates typed as NAP1 had tcdA, tcdB, binary toxin gene cdtB and tcdC deletion. All isolates were resistant to clindamycin, fluoroquinolones and rifampicin. Under this scenario, surveillance programmes for CDI should be implemented in public health facilities in Latin America and diagnosis of CDI should be considered, especially in patients with predisposing factors.
Novel three-dimensional coordination polymers of lanthanides with sulfate and oxydiacetic acid
Authors: Prasad Thazhe Kootteri , Rajasekharan M. V.
Published: November 2013

Three three-dimensional coordination polymers,viz.poly[[diaqua-μ4-oxydiacetato-di-μ4-sulfato-dipraseodymium(III)] hemihydrate], [Pr2(C4H4O5)(SO4)2(H2O)2]·0.5H2O, (I), poly[[diaquadi-μ3-oxydiacetato-μ3-sulfato-dineodymium(III)] 1.32-hydrate], [Nd2(C4H4O5)2(SO4)(H2O)2]·1.32H2O, (II), and poly[[diaquadi-μ3-oxydiacetato-μ3-sulfato-disamarium(III)] 1.32-hydrate], [Sm2(C4H4O5)2(SO4)(H2O)2]·1.32H2O, (III), were obtained by hydrothermal reactions of the respective lanthanide oxides and ZnSO4with oxydiacetic acid (odaH2). The Nd3+and Sm3+compounds form isomorphous crystal structures in which the lanthanide cations are nine-coordinate, having a tricapped trigonal prismatic coordination. The Pr3+compound has an entirely different crystal structure in which two types of coordination polyhedra are observed,viz.nine-coordinate (trigonal prism) and ten-coordinate (bicapped square antiprism). The sulfate anions show various coordination modes, one of which has only rarely been observed crystallographically to date.
2-[(E)-2-(4-Methoxyphenyl)ethenyl]-1-methylpyridinium iodide
Authors: Senthil K. , Kalainathan S. , RubanKumar A. , Ramkumar V. , Podder Jiban
Published: November 2013

In the title molecular salt, C16H10NO+·I−, the dihedral angle between the pyridinium and benzene rings is 6.61 (8)°. In the crystal, the cation is linked to the anion by a C—H...I interaction arising from the activated aromatic C atom adjacent to the N+cation.
(S)-4,5-Diphenyl-1-[1-phenyl-3-(phenylsulfanyl)propan-2-yl]-2-(thiophen-2-yl)-1H-imidazole
Authors: Gao Jie , Wang Hongyan , Yang Liangru , Xiao Yongmei , Mao Pu
Published: November 2013

In the title compound, C34H28N2S2, the central imidazole ring (r.m.s. deviation = 0.0015 Å) forms dihedral angles of 55.7 (3), 17.94 (11) and 86.27 (11)°, respectively, with the mean planes of the attached thienyl and two phenyl substituents. The thienyl ring shows ring-flip disorder [occupancy ratio = 0.647 (2):0.353 (2)]. The chiral centre maintains theSconfiguration of the L-phenylalaninol starting material. Intra- and intermolecular C—H...S hydrogen bonds involving the disordered thienyl ring are observed.
N-(1-Allyl-1H-indazol-5-yl)-4-methylbenzenesulfonamide
Authors: Chicha Hakima , Rakib El Mostapha , Abderrafia Hafid , Saadi Mohamed , El Ammari Lahcen
Published: November 2013

The asymmetric unit of the title compound, C17H17N3O2S, contains two independent molecules linked by an N—H...O hydrogen bond. The molecules show different conformations. In the first molecule, the fused five- and six-membered ring system is almost perpendicular to the plane through the atoms forming the allyl group, as indicated by the dihedral angle of 85.1 (4)°. The dihedral angle with the methylbenzenesulfonamide group is 78.8 (1)°. On the other hand, in the second molecule, the dihedral angles between the indazole plane and the allyl and methylbenzenesulfonamide groups are 80.3 (3) and 41.5 (1)°, respectively. In the crystal, molecules are further linked by N—H...N and C—H...O hydrogen bonds, forming a three-dimensional network.
Niche filtering rather than partitioning shapes the structure of temperate forest ant communities
Authors: Fowler David , Lessard Jean‐Philippe , Sanders Nathan J.
Published: November 2013

An ever‐increasing number of studies use tools from community phylogenetics to infer the processes underlying the assembly of communities. However, very few studies simultaneously use experimental approaches to characterize the ecological niches of species and directly assess the importance of these structuring processes.

In this study, we developed an experimental approach for quantifying the use of four types of food resources and three habitat templets in temperate forest ant assemblages. We then used null models to assess whether niches overlapped more or less than expected by chance. Finally, we integrated comparative phylogenetic methods with experimental data on niche use to assess the degree of phylogenetic signal in several key components of the niche.

We found that niche filtering, rather than partitioning, was the predominant structuring force. Niche filtering resulted from conservatism in habitat niches in evolutionary time and limitations in the availability of food resources in ecological time.

Our study thus supports the idea that similarities in niches among species, rather than the differences, drive the assembly of ant communities.
Estimating the consequences of multiple threats and management strategies for semi‐aquatic turtles
Authors: Crawford Brian A. , Maerz John C. , Nibbelink Nathan P. , Buhlmann Kurt A. , Norton Terry M.
Published: November 2013

Roads are pervasive fixtures on most landscapes but are typically among many factors contributing to wildlife population declines. Addressing road mortality as part of larger conservation efforts is challenging because it can be difficult to measure per capita mortality from roads and other concurrent threats.

We used 4 years of mark–recapture–recovery data for diamondback terrapins Malaclemys terrapin on a causeway in Georgia, USA, to directly estimate threats of adult road mortality and nest predation, contrast the consequences to population growth using stage‐based matrix models and make management recommendations to stabilize the population.

Mean estimated annual adult road mortality was 11·1% (range = 4·4–16·4%). Estimated annual nest predation was 61·9%. We estimated that the population was declining (λ < 0·98) in all scenarios where both threats were included. Variation in adult survival was the most influential (highest elasticity) contributor to population growth relative to other demographic rates; however, λ would remain below 1 with any nest predation rate exceeding our estimate even if actions to mitigate road mortality were 100% effective.

Synthesis and applications. Our study provides some of the first direct estimates of vehicle mortality rates and shows that mortality can remain sufficiently high among years to cause population declines. We also demonstrate that management actions focused on singular threats are inadequate for recovering populations. We conclude that integrated road and predator management is necessary to conserve turtle populations, and we suggest alternative strategies to compensate for some vehicle mortality and nest depredation.
Hot spots and hot moments of diamondback terrapin road‐crossing activity
Authors: Crawford Brian A. , Maerz John C. , Nibbelink Nathan P. , Buhlmann Kurt A. , Norton Terry M. , Albeke Shannon E.
Published: November 2013

Road mortality is a major component of human impacts on wildlife populations, and the pervasiveness of roads on the landscape presents a substantial challenge for managing those impacts. The feasibility of methods to reduce road mortality depends on the degree to which this threat is spatially or temporally concentrated, which can be based on habitat, human activities or species' ecology. Diamondback terrapinsMalaclemys terrapinare a species of conservation concern across their range, and road mortality is a major threat contributing to local population declines.

We used intensive road surveys of the 8·7‐kmDowning‐MusgroveCauseway toJekyllIsland,Georgia,USA, over 2 years to determine whether road activity and mortality was diffused or concentrated spatially (hot spots) or temporally (hot moments) in order to guide efficient management.

In 2009 and 2010, we documented 636 terrapin crossings that were temporally and spatially condensed. Temporally, there was a 70–80% chance of a terrapin occurring on the road within a 3‐h period around the diurnal high tide and within the first 30 days of the ˜75 day nesting season. Over the two nesting seasons, 52% of terrapin occurrences on the road occurred within the 3‐h period around high tide. Spatially, 30% of terrapins were observed crossing in three hot spots that composed less than 10% of the length of the entire causeway, and the percentage of unvegetated high marsh was negatively associated with the number of terrapins that occurred on a section of road.

Synthesis and applications. Our results demonstrate that hot spots and hot moments can be identified for species at finer scales than those found by other studies and are related, strongly or weakly, to specific temporal processes or habitat features. We found patterns of road mortality, like most threats, can be diffused or concentrated; therefore, complementary management tools that focus on hot spots or moments and also address the more diffused component of road mortality will be required to reduce this threat for at‐risk wildlife.
Stability, genotypic and phenotypic diversity of Shewanella baltica in the redox transition zone of the Baltic Sea
Authors: Deng Jie , Brettar Ingrid , Luo Chengwei , Auchtung Jennifer , Konstantinidis Konstantinos T. , Rodrigues Jorge L. M. , Höfle Manfred , Tiedje James M.
Published: November 2013

Studying how bacterial strains diverge over space and time and how divergence leads to ecotype formation is important for understanding structure and dynamics of environmental communities. Here we assess the ecological speciation and temporal dynamics of a collection of Shewanella baltica strains from the redox transition zone of the central Baltic Sea, sampled at three time points over a course of 12 years, with a subcollection containing 46 strains subjected to detailed genetic and physiological characterization. Nine clades were consistently recovered by three different genotyping approaches: gyrB gene sequencing, multilocus sequence typing (MLST) and whole genome clustering of data from comparative genomic hybridization, and indicated specialization according to nutrient availability, particle association and temporal distribution. Genomic analysis suggested higher intra‐ than inter‐clade recombination that might result from niche partitioning. Substantial heterogeneity in carbon utilization and respiratory capabilities suggested rapid diversification within the same ‘named’ species and physical habitat and showed consistency with genetic relatedness. At least two major ecotypes, represented by MLST clades A and E, were proposed based on genetic, ecological and physiological distinctiveness. This study suggests that genetic analysis in conjunction with phenotypic evaluation can provide better understanding of the ecological framework and evolutionary trajectories of microbial species.