bluuebunny/crossref_metadata_2025 huggingface dataset:
Public Participation and Water Use Rights
Authors: King P , Reddell C
Published: January 2016

The conservation and protection of water resources is paramount in the safeguarding of environmental rights and the attainment of sustainable development in South Africa. Although the National Water Act 36 of 1998 (the NWA) seeks to provide a framework for ensuring the sustainable use of water resources, its application has been hindered by capacity and enforcement constraints, a legacy of water pollution (primarily as a result of mining and industrial activities), and poor resource management. To aggravate this situation, the difficulties in effectively implementing the NWA are exacerbated by inadequate public participation in water use licensing processes. Public participation in environmental decision-making has increasingly received recognition for its role in ensuring administrative justice and the protection of environmental rights. While environmental legislation (in many cases) sets out procedures for ensuring that public views are taken into account in environmental decision-making processes, the judiciary has also recognised the pivotal role of public engagement in ensuring administrative justice where environmental rights are at stake. Sound public participation practices play an important role in identifying issues requiring consideration in the context of environmental assessment processes, as well as in ensuring that communities are empowered to monitor, identify and report on potential contraventions of environmental legislation. Water is a vital natural resource which is under significant pressure in South Africa. In the circumstances, effective public participation is crucial to ensuring the protection and equitable use of water resources. It follows that provision for comprehensive public engagement in water use licensing processes is integral to ensuring the sustainable management of water resources. While provision is made in the NWA for public engagement in the context of water use licensing processes, such participation is limited, and in some cases discretionary. This, in turn, has the effect of curtailing the right to an administrative appeal in respect of a decision by the competent authority to grant water use rights. This paper will explore the role of public participation in environmental decision-making with a view to identifying the shortcomings of the NWA in this regard, as well as the effectiveness of the Promotion of Administrative Justice Act 3 of 2000 (the PAJA) in supplementing the NWA's shortcomings. It will also consider the implications which recent changes to South Africa's environmental legal framework will have for public participation in water use licensing, particularly in the context of mining-related activities.
Public-private Partnerships in Local Disaster Management: A Panacea to all Local Disaster Management Ills?
Authors: Van der Berg A
Published: January 2016

It is anticipated that the occurrence and intensity of disasters will increase globally and in South Africa where typical disasters include droughts, floods, extreme hailstorms, gales, fires and earthquakes, as well as sinkholes arising from mining activity in dolomitic areas. Disasters such as these result in human suffering and damage to the resources and infrastructure on which South Africans rely for their survival and the maintenance of their quality of life. Section 24 of the Constitution of the Republic of South Africa, 1996 affords to everyone the right to an environment that is not harmful to his or her health and well-being. It may be argued that a person's sense of environmental security in relation to the potential risks and dangers of disaster falls within the scope of the protection provided by section 24. The responsibility to intervene for the protection of the interests inherent in the constitutional environmental right lies with the government of South Africa. Disaster management specifically is a functional area of competence of national and provincial government, but practice has shown that the actual implementation of and planning for disaster management happens in the local government sphere. Against the backdrop of these introductory discussions and, given the fact that several municipalities in South Africa are under-resourced, this article very specifically aims to critically discuss and describe from a legal perspective the potential and function of public-private partnerships (PPPs) between local government (municipalities) and the private sector (such as industries) in fulfilling the legally entrenched disaster management mandate of municipalities. Through a critical evaluation of some existing PPPs, this article illustrates that the private sector has a key role to play in assisting municipalities to fulfil their legally entrenched disaster management mandate.
Judicial "Translation" and Contextualisation of Values: Rethinking the Development of Customary Law in Mayelane
Authors: Lewis I
Published: January 2016

The relevance of Mayelane v Ngwenyama (2013 4 SA 415 (CC)) has not been exhausted. Particularly the constitutional mandate undertaken by the Constitutional Court to "develop" customary law deserves closer scrutiny. In Mayelane the Constitutional Court, in seeking to vindicate the dignity and equality of women in polygynous marriages, examines the validity of a second marriage in terms of "living" customary law. The Court applies customary law as a "primary" source of law, while it simultaneously promotes the values enshrined in the Constitution, however – bearing in mind that the constitutional values of dignity and equality have their roots in international rights law – the Court is in reality dealing with normative plurality spanning subnational (customary), national as well as international regimes. Furthermore, each of these systems is embedded in its own socio-cultural context, and therefore the liberal individualism of international law could be "foreign" in a customary context, which values communalism. Hence, it is asked whether courts can accommodate pluralism by simply transposing norms and values such as dignity and equality from one system to another, particularly in cases where the court sets out to "develop" customary law. It is argued that norms and values have to be interpreted and applied with reference to their particular context and audience. Thus, there is a need for courts to contextualise and attune, or "translate" norms, whenever they are applied to another system.
Persistence of upper stratospheric winter time tracer variability into the Arctic spring and summer
Authors: Siskind David E. , Nedoluha Gerald E. , Sassi Fabrizio , Rong Pingping , Bailey Scott M. , Hervig Mark E. , Randall Cora E.
Published: January 2016

Abstract. Using data from the Aeronomy of Ice in the Mesosphere (AIM) and the Aura satellites, we have categorized the interannual variability of winter and spring time upper stratospheric CH4. We further show the effects of this variability on the chemistry of the upper stratosphere throughout the following summer. Years with strong mesospheric descent followed by dynamically quiet springs, such as 2009, lead to the lowest summertime CH4. Years with relatively weak descent, but strong springtime planetary wave activity, such as 2011, have the highest summertime CH4. By sampling the Aura Microwave Limb Sounder according to the occultation pattern of the AIM Solar Occultation for Ice Experiment, we show that summertime upper stratospheric ClO almost perfectly anticorrelates with the CH4. This is consistent with the reaction of atomic chlorine with CH4 to form the reservoir species, HCl. The summertime ClO for years with strong, uninterrupted mesospheric descent is about 50 % greater than in years with strong horizontal transport and mixing of high CH4 air from lower latitudes. Small, but persistent effects on ozone are also seen such that between 1–2 hPa, ozone is about 4–5 % higher in summer for the years with the highest CH4 relative to the lowest. This is consistent with the role of the chlorine catalytic cycle on ozone. These dependencies may offer a means to monitor dynamical effects on the high latitude upper stratosphere using summertime ClO measurements as a proxy. Also, these chlorine controlled ozone decreases, which are seen to maximize after years with strong uninterrupted wintertime descent, represent a new mechanism by which mesosospheric descent can affect polar ozone. Finally, given that the effects on ozone appear to persist much of the rest of the year, the consideration of winter/spring dynamical variability may also be relevant in studies of ozone trends.
Impact of buildings on surface solar radiation over urban Beijing
Authors: Zhao B. , Liou K. N. , Gu Y. , He C. , Lee W. L. , Chang X. , Li Q. B. , Wang S. X. , Tseng H. R. , Leung L. R. , Hao J. M.
Published: January 2016

Abstract. The rugged surface of an urban area due to varying buildings can interact with solar beams and affect both the magnitude and spatiotemporal distribution of surface solar fluxes. Here we systematically examine the impact of buildings on downward surface solar fluxes over urban Beijing by using a 3-D radiation parameterization that accounts for 3-D building structures versus the conventional plane-parallel scheme. We find that the resulting downward surface solar flux deviations between the 3-D and the plane-parallel schemes are generally ±1–10 W m−2 at 800-m grid resolution and within ±1 W m−2 at 4-km resolution. Pairs of positive negative flux deviations on different sides of buildings are resolved at 800-m resolution, while they offset each other at 4-km resolution. Flux deviations from the unobstructed horizontal surface at 4-km resolution are positive around noon but negative in the early morning and late afternoon. The corresponding deviations at 800-m resolution, in contrast, show diurnal variations that are strongly dependent on the location of the grids relative to the buildings. Both the magnitude and spatiotemporal variations of flux deviations are largely dominated by the direct flux. Furthermore, we find that flux deviations can potentially be an order of magnitude larger by using a finer grid resolution. Atmospheric aerosols can reduce the magnitude of downward surface solar flux deviations by 10–65 %, while the surface albedo generally has a rather moderate impact on flux deviations. The results imply that the effect of buildings on downward surface solar fluxes may not be critically significant in mesoscale atmospheric models with a grid resolution of 4 km or coarser. However, the effect can play a crucial role in meso-urban atmospheric models as well as microscale urban dispersion models with resolutions of 1 m–1 km.
A review of sources of systematic errors and uncertainties in observations and simulations at 183GHz
Authors: Brogniez Hélène , English Stephen , Mahfouf Jean-François , Behrendt Andreas , Berg Wesley , Boukabara Sid , Buehler Stefan Alexander , Chambon Philippe , Gambacorta Antonia , Geer Alan , Ingram William , Kursinski E. Robert , Matricardi Marco , Odintsova Tatyana , Payne Vivienne , Thorne Peter , Tretyakov Mikhail , Wang Junhong
Published: January 2016

Abstract. Several recent studies have observed biases between measurements in the 183.31GHz water vapour line by space-borne sounders and calculations using radiative transfer models with inputs from either radiosondes (RAOBS) or short range forecasts by Numerical Weather Prediction (NWP) models. This paper discusses all the relevant categories of observation-based or model-based data, quantification of their uncertainties, and separation of biases that could be common to all causes from those attributable to a particular cause. Reference observations from radiosondes, Global Navigation Satellite Systems (GNSS), Differential Absorption Lidar (DIAL) and Raman lidar are thus overviewed. Biases arising from their procedures of calibration, NWP models and data assimilation, instrument biases and radiative transfer models (both the models themselves and the underlying spectroscopy) are presented and discussed. Although no single process in the comparisons seems capable of explaining the observed structure of bias, recommendations are made in order to better understand the causes.
Equatorward phytoplankton migration during a cold spell within the Late Cretaceous supergreenhouse
Authors: van Helmond Niels A.G.M. , Sluijs Appy , Papadomanolaki Nina M. , Plint A.Guy , Gröcke Darren R. , Pearce Martin A. , Eldrett James S. , Trabucho-Alexandre João , Walaszczyk Ireneusz , van de Schootbrugge Bas , Brinkhuis Henk
Published: January 2016

Abstract. Oceanic Anoxic Event 2 (OAE2), a ~600 kyr episode close to the Cenomanian-Turonian boundary (ca. 94 Ma), is characterized by widespread marine anoxia and ranks amongst the warmest intervals of the Phanerozoic. The early stages of OAE2 are, however, marked by an episode of widespread transient cooling and bottom water oxygenation: the Plenus Cold Event. This cold spell has been linked to a decline in atmospheric pCO2, resulting from enhanced global organic carbon burial. To investigate the response of phytoplankton to this marked and rapid climate shift we examined the biogeographical response of dinoflagellates to the Plenus Cold Event. Our study is based on a newly generated geochemical and palynological dataset from a high-latitude Northern Hemisphere site, Pratts Landing (western Alberta, Canada). We combine this data with a semi-quantitative global compilation of the stratigraphic distribution of dinoflagellate cyst taxa. The data show that dinoflagellate cysts grouped in the Cyclonephelium compactum-membraniphorum morphological plexus migrated from high- to mid-latitudes during the Plenus Cold Event, making it the sole widely found (micro)fossil to mark this cold spell. In addition to earlier reports from regional metazoan migrations during the Plenus Cold Event, our findings illustrate the effect of rapid climate change on the global biogeographical dispersion of phytoplankton.
Testing the impact of stratigraphic uncertainty on spectral analyses of sedimentary series
Authors: Martinez Mathieu , Kotov Sergey , De Vleeschouwer David , Pas Damien , Pälike Heiko
Published: January 2016

Abstract. Spectral analysis is a key tool for identifying periodic patterns in sedimentary sequences, including astronomically related orbital signals. While most spectral analysis methods require equallyspaced samples, this condition is rarely achieved either in the field or when sampling sediment cores. Here, we propose a method to assess the impact on the resulting power spectra of the uncertainty or error made in the measurement of sample stratigraphic position. We apply a Monte-Carlo procedure to randomise the sample steps of depth series using a gamma distribution. Such a distribution preserves the stratigraphic order of samples, and allows control of the mean and variance of the sample step distribution after randomisation. We test the Monte-Carlo procedure on two geological datasets and find that at 5 % uncertainty in the sample positions, the power of the spectral peaks is signifi cantly affected in all frequencies above ~1/3 of the Nyquist frequency. The randomisation process progressively affects the lower frequencies when increasing the level of uncertainty in the sample position. With 10 % sample position uncertainty, the change in relative power exceeds 10 % in all frequencies above ~1/5 of the Nyquist frequency. For robust applications of the power spectrum, we suggest strongly controlling the measurement of the sample position, keeping the variance of the sample distribution to a maximum of 10 % of the average sample step. In addition, the simulations indicate that taking at least 6-10 samples per precession cycle should allow calculation of robust power spectra estimates in the Milankovitch band.
A flexible importance sampling method for integrating subgrid processes
Authors: Raut E. K. , Larson V. E.
Published: January 2016

Abstract. Numerical models of weather and climate need to compute grid-box-averaged rates of physical processes such as microphysics. These averages are computed by integrating subgrid variability over a grid box. For this reason, an important aspect of atmospheric modeling is spatial integration over subgrid scales. The needed integrals can be estimated by Monte Carlo integration. Monte Carlo integration is simple and general but requires many evaluations of the physical process rate. To reduce the number of function evaluations, this paper describes a new, flexible method of importance sampling. It divides the domain of integration into eight categories, such as the portion that contains both precipitation and cloud, or the portion that contains precipitation but no cloud. It then allows the modeler to prescribe the density of sample points within each of the eight categories. The new method is incorporated into the Subgrid Importance Latin Hypercube Sampler (SILHS). The resulting method is tested on drizzling cumulus and stratocumulus cases. In the cumulus case, the sampling error can be considerably reduced by drawing more sample points from the region of rain evaporation.
Effect of soil coarseness on soil base cations and available micronutrients in a semi-arid sandy grassland
Authors: Lü L. , Wang R. , Liu H. , Yin J. , Wang Z. , Zhao Y. , Yu G. , Han X. , Jiang Y.
Published: January 2016

Abstract. Soil coarseness is the main process decreasing soil organic matter and threatening the productivity of sandy grasslands. Previous studies demonstrated negative effect of soil coarseness on soil carbon storage, but less is kn own about how soil base cations (exchangeable Ca, Mg, K, and Na) and available micronutrients (available Fe, Mn, Cu, and Zn) response to soil coarseness. In a semi-arid grassland of northern China, a field experiment was initiated in 2011 to mimic the effect of soil coarseness on soil base cations and available micronutrients by mixing soil with different mass proportions of sand: 0 % coarse elements (C0), 10 % (C10), 30 % (C30), 50 % (C50), and 70 % (C70). Soil coarseness significantly increased soil pH in three soil depths of 0–10 cm, 10–20 cm and 20–40 cm with the highest pH values detected in C50 and C70 treatments. Soil fine particles (smaller than 0.25 mm) significantly decreased with the degree of soil coarseness. Exchangeable Ca and Mg concentrations significantly decreased with soil coarseness degree by up to 29.8 % (in C70) and 47.5 % (in C70), respectively, a cross three soil depths. Soil available Fe, Mn and Cu significantly decreased with soil coarseness degree by 62.5 %, 45.4 % and 44.4 %, respectively. As affected by soil coarseness, the increase of soil pH, decrease of soil fine particles (including clay), and decline in soil organic matter were the main driving factors for the decrease of exchangeable base cations (except K) and available micronutrients (except Zn) through soil profile. Developed under soil coarseness, the loss and redistribution of base cations and available micronutrients along soil depths might pose threat to ecosystem productivity of this sandy grassland.
Delineating small karst watersheds based on digital elevation model and eco-hydrogeological principles
Authors: Luo G. J. , Wang S. J. , Bai X. Y. , Liu X. M. , Chen A. Y.
Published: January 2016

Abstract. Dominated by specific eco-hydrogeological backgrounds, a small watershed delineated by using the traditional method is always inauthentic in karst regions because it cannot accurately reflect the eco-hydrological process of the dual structure of the surface and subsurface. This study proposes a new method for the delineation of small watersheds based on digital elevation model (DEM) and eco-hydrogeological principles in karst regions. This method is applied to one section of the tributary area (Sancha River) of the Yangtze River in China. By comparing the quantity, shape, superimposition, and characteristics of the internal hydrological process of a small watershed extracted by using the digital elevation model with that extracted by using the proposed method of this study, we conclude that the s mall karst watersheds extracted by the new method accurately reflect the hydrological process of the river basin. Furthermore, we propose that the minimum unit of the river basin in karst regions should be the watershed whose exit is the corrosion–erosion datum and a further division of watershed may cause a significant inconsistency with the true eco-hydrological process.
Analysis of Causative Microorganism in 248 Primary Hip Arthroplasties Revised for Infection: A Study Using the NJR Dataset
Authors: Holleyman Richard J. , Baker Paul N. , Charlett Andre , Gould Kate , Deehan David J.
Published: January 2016

Introduction

This study aimed to describe the epidemiology of the causative organism in a series of primary hip arthroplasties revised for a diagnosis of periprosthetic joint infection (PJI) in England and Wales.

Methods

Patient data from the National Joint Registry (NJR) was linked to microbiology data held by Public Health England (PHE) which identified a series of 248 primary hip arthroplasties revised for PJI between 2003 and 2014. Definitive cultures, isolated at time of revision surgery, were available for all cases. Total hip arthroplasty (n = 239, 96%) and hip resurfacing (n = 5, 2%) were the most commonly performed primary procedures. A two-stage revision was the most common operative management (n = 174, 70%).

Results

202 (81%) cases were infected with a single genus microorganism and the most commonly implicated genus was Staphylococcus species (70% of all single genus infections). Staphylococcus species were also the most commonly identified microorganism in mixed genus infections (74% of patient's cultures). There was a significant difference in microorganism distribution when comparing uncemented vs cement implant fixation, with a higher incidence of Gram-negative infection observed in the uncemented group (p = 0.048, Chi-square).

Conclusions

Both prophylactic and therapeutic antibiotic regimes should be focused on targeting Staphylococci.
Distribución local de la inversión de decisión regional: el caso del FNDR en Chile 1997-2012
Authors: Muñoz José Miguel
Published: January 2016

Esta investigación busca determinar los factores que inciden en que una comuna tenga una mayor o menor asignación de recursos vía proyecto FNDR, dentro de las regiones de Chile, para el período 1997-2012, a través de una metodología cuantitativa. Se concluye que si bien el FNDR es eficaz en propender a una equidad interregional, no lo es al momento de propender a una equidad intra-regional, lo que abre espacio para la innovación institucional.
Participación en la formulación de políticas culturales. El caso del Consejo Nacional de la Cultura y las Artes (CNCA) durante 2011-2016
Authors: Moreno Paola
Published: January 2016

El objetivo de esta investigación es analizar la trayectoria de los instrumentos de participación en el proceso de formulación de políticas públicas culturales 2011- 2016, identificando si hay cambios en los mecanismos institucionales y normativos que aplica el Estado para implementar los principios orientadores de las políticas culturales en Chile, además de establecer sus actores y procedimientos. El estudio de caso es de tipo exploratorio descriptivo, con uso de metodología cualitativa, mediante el análisis de documentación secundaria institucional. Se concluye que el cambio de signo político del gobierno de turno impacta en la orientación de las políticas en cultura. Asimismo existe un desempeño limitado de la participación de la sociedad civil en el Directorio, pudiéndose avanzar tanto el fortalecimiento de la participación como en la generación de mecanismos que promuevan una mayor apertura de la Administración, a través de la incorporación del ciudadano no organizado, creando una red más abierta y plural, aumentando así el carácter democrático de la relación Estado-Sociedad Civil.
Effect of Recombination between a Molecular Ion and an Electron on Radial Dose in the Irradiation of a Heavy Ion
Authors: Moribayashi Kengo
Published: January 2016

This paper discusses the effect of recombination between a molecular ion and a free electron on radial dose in the irradiation of a heavy ion through simulations. This irradiation produces molecular ions and free electrons due to the heavy ion impact ionization. The composition electric field, which is formed from these molecular ions, traps some of free electrons and these trapped free electrons increase radial dose near the heavy ion path. These trapped electrons also cause the recombination and that the recombination enhances radial dose.
Aggregating Fuzzy QL- and (S,N)-Subimplications: Conjugate and Dual Constructions
Authors: Reiser Renata Hax Sander , Benítez Íbero C. K. , Yamin Adenauer C. , Bedregal Benjamín R. C.
Published: January 2016

Fuzzy (S,N)- and QL-subimplication classes can be obtained by a distributive n-ry aggregation  performed over the families of t-subnorms and t-subconorms along with a fuzzy negation. Since these classes of subimplications are explicitly represented by t-subconorms and t-subnorms verifying the generalized associativity, the corresponding (S,N)- and QL-subimplications,  referred as I(S,N) and I_(S,T,N), are  characterized as distributive n-ary aggregation together with related generalizations as the exchange and neutrality principles. Based on these results, the both subclasses I_(S,n) and I_QL of (S,N)- and QL-subimplications which are obtained by the median aggregation operation performed over the standard negation N_S together with  the families  of t-subnorms and t-subconorms S_P and T_P, respectively. In particular, the subclass T_P extends the product t-norm T_P as well as S_P extends the algebraic sum S_P. As the main results, the family of subimplications I_(S_P,N) and I_(S_P,T_P,N) extends the implication class by preserving the corresponding properties. We also present an extension from (S,N)- and QL-subimplications to (S,N)- and QL-implications and discuss dual and conjugate constructions.
Rubroboletus le-galiae (Boletales, Basidiomycota), a species new for Poland
Authors: Halama Marek
Published: January 2016

Rubroboletus le-galiae is reported for the first time from Poland. Macro- and micromorphological characters of the species are described and illustrated based on the study of material collected at three microlocalities in Łężczok reserve (SW Poland). The delimitation of R. le-galiae from related species of the genus Rubroboletus (R. satans, R. rubrosanguineus, R. rhodoxanthus) is shortly discussed and the knowledge of its ecology and distribution is briefly summarized.
Preliminary studies of fungi in the Biebrza National Park (NE Poland). Part III. Micromycetes – new data
Authors: Ruszkiewicz-Michalska Malgorzata , Bałazy Stanisław , Chełkowski Jerzy , Dynowska Maria , Pawłowska Julia , Sucharzewska Ewa , Szkodzik Jarosław , Tkaczuk Cezary , Wilk Mateusz , Wrzosek Marta
Published: January 2016

Ecological information concerning 292 fungal taxa is reported as a result of two surverys in the Biebrza National Park. Most data presented come from the 5-day all-fungi inventory of the Polish Mycological Society in 2013, and 47 species were recorded during studies in the Biele Suchowolskie fen in 2008/2009. In total, 27 species of zygomycetes, 232 ascomycetes (including anamorphs) and 27 basidiomycetes (mainly Pucciniales). Additionaly some representatives of fungi-like organisms from Stramenopiles (4 species) and Dictyostelia (2) were identified. Fungal groups included were the same as in the previous survey in 2012: 190 taxa associated with plants, 15 with animals, 8 with fungi and 71 isolated from soil, plant debris and animal excrements. The most numerous were anamorphic ascomycetes (159 species). Nineteen species have not been previously known from Poland and 31 species are rare (1–3 localities). For the Biebrza National Park 197 species (67.5%) are new.
Non-lipophilic mycobiota of human skin
Authors: Talaga Katarzyna , Krzyściak Paweł
Published: January 2016

The human skin is inhabited by many species of bacteria and fungi, which are its natural microbiota. Fungi colonizing the skin, including those causing disease, characterized by great variety and variability, can be influenced by various factors. The purpose of this study was to investigate the composition of the non-lipid-dependent fungal microbiota of skin, including the presence of species potentially pathogenic for humans. Fifty-six volunteers of both sexes aged 22–78 were subjected to the study. Swabs were taken from the face, chest, back and interdigital spaces of hands. Mycobiota isolated proved to vary both in terms of the location of occurrence and gender of patients. Interdigital spaces of hands, dominated by yeasts, constitute a location on human skin most contaminated with fungi. Molds were more often isolated from the face and chest. The back was the least contaminated location. There was no difference in fungal incidence in relation to sex.
Biology, cultivation, and medicinal functions of the mushroom Hericium erinaceum
Authors: Sokół Sławomir , Golak-Siwulska Iwona , Sobieralski Krzysztof , Siwulski Marek , Górka Katarzyna
Published: January 2016

Hericium erinaceum (Bull.: Fr.) Pers. is an edible fungus of great significance in medicine. It is rarely found in Europe, in contrast, it is common in Japan and North America. Its fruitbodies have been well-known for hundreds of years in traditional Chinese medicine and cuisine. A cradle of H. erinaceum cultivation is Asia. In Eastern Europe is rare in natural habitats, but can be successfully cultivated. Both fruitbodies and mycelia are rich in active, health promoting substances. Tests of substances extracted from this mushroom carried out on animals and in vitro have given good results. They can be used in the treatment of cancer, hepatic disorders, Alzheimer’s and Parkinson’s diseases, wound healing. They improve cognitive abilities, support the nervous and immune systems. Promising results have been reported in clinical trials and case reports about the human treatment (e.g., recovery from schizophrenia, an improvement of the quality of sleep, alleviation of the menopause symptoms). The subject of this paper is to summarize information about the development of mycelium, the best conditions for cultivation of fruitbodies, bioactive substances and their use in medicine.
Determination of Free and Total Choline and Carnitine in Infant Formula and Adult/Pediatric Nutritional Formula by Liquid Chromatography/Tandem Mass Spectrometry (LC/MS/MS): Single-Laboratory Validation, First Action 2015.10
Authors: Ellingson David J , Shippar Jeffrey J , Gilmore Justin M
Published: January 2016

Analytical methods for the analysis of both L-carnitine and choline are needed for reliable and accurate determination in infant formula and adult/pediatric nutritional formula. These compounds are different in how they are utilized by the human body, but are structurally similar. L-carnitine and choline are quaternary ammonium compounds, enabling both to be retained under acidic conditions with strong cation exchange (SCX) chromatography. This method analyzes both compounds simultaneously as either the free forms or as a total amount that includes bound sources such as phosphatidylcholine or acetylcarnitine. The free analysis consists of water extraction and analysis by LC/MS/MS, while the total analysis consists of extraction by acid assisted microwave hydrolysis and analysis by LC/MS/MS. Calibration standards used for calculations are extracted with all samples in the batch. A single laboratory validation (SLV) was performed following the guidelines of the AOAC Stakeholder Panel on Infant Formula and Adult Nutritionals (SPIFAN) utilizing the kit of materials provided. The results achieved meet the requirements of SMPR 2012.010 and 2012.013 for L-carnitine and total choline, respectively.
Development of Singlet Oxygen Absorption Capacity (SOAC) Assay Method Using a Microplate Reader
Authors: Takahashi Shingo , Iwasaki-Kino Yuko , Aizawa Koichi , Terao Junji , Mukai Kazuo
Published: January 2016

Recently, a new assay method that can quantify the singlet oxygen absorption capacity (SOAC) of natural antioxidants and food extracts was developed. The SOAC values were measured in ethanol–chloroform–D2O (50 + 50 + 1, v/v/v) solution at 35°C using a UV-Vis spectrophotometer equipped with a six-channel cell positioner and an electron-temperature control unit. In the present study, measurement of the SOAC values was performed for eight representative carotenoids and three vegetable extracts (tomato, carrot, and red paprika) using a versatile instrument, the microplate reader. A 24-well glass microplate was used for measurements because a plastic microplate, commonly used in the laboratory, dissolves in the ethanol–chloroform–D2O solution. The SOAC values of eight carotenoids and three vegetable extracts measured using a microplate reader were in good agreement with the corresponding values measured using a UV-Vis spectrophotometer, suggesting that the microplate reader is an applicable instrument for the measurement of reliable SOAC values for general antioxidants and food extracts in solution.
Simultaneous Determination of Piperine, Capsaicin, and Dihydrocapsaicin in Korean Instant-Noodle (Ramyun) Soup Base Using High-Performance Liquid Chromatography with Ultraviolet Detection
Authors: Shim You-Shin , Kim Jong-Chan , Jeong Seung-Weon
Published: January 2016

A simultaneous analytical method for piperine, capsaicin, and dihydrocapsaicin in Korean instant-noodle soup base using HPLC was validated in terms of precision, accuracy, sensitivity, and linearity. The HPLC separation was performed on a reversed-phase C18 column (5 μm particle size, 4.6 mm id, 250 mm length) using a UV detector fixed at 280 nm. The LOD and LOQ of the HPLC analyses ranged from 0.25 to 1.03 mg/kg. The intraday and interday precisions of the individual piperine, capsaicin, and dihydrocapsaicin were <10.55%, and the recovery values ranged from 85.43 to 94.68%. The calibration curves exhibited good linearity (r2 = 0.999) within the tested ranges. These results suggest that the analytical method in this study can be used to classify Korean instant noodles based on their levels of spiciness.
Validation of FoodChek™ - Salmonella for Rapid Detection of Salmonella in Eggs, Derivative Products, and the Environment
Authors: Buzinhani Melissa , Tremblay Renaud , Martinez Gabriela , Giuffre Michael , Hammack Thomas , Fernandez Maria Cristina , Ziemer Wayne
Published: January 2016

The FoodChek™ - Salmonella assay is an immunomagnetic lateral flow assay for the rapid detection (shorter than 24 h) of the most frequently isolated Salmonella (groups B–E) in eggs, egg-derivative products, and environmental surfaces. The FoodChek - Salmonella assay correctly identified 99.6% (239/240) of the samples tested in the matrix studied, and the statistical analysis of the method comparison study results demonstrated that it performs as well as U.S. culture-based reference methods. Ninety-nine percent of the 103 Salmonella strains tested belonging to serogroups B–E were detected during the inclusivity study. Concerning the exclusivity, 31 nontarget strains were tested. No cross-reactivity was observed in FoodChek - Salmonella assay enrichment conditions. In addition, the assay shows strong robustness, good stability, and consistency among lots. The present study proves that the assay is an effective tool for the rapid detection of Salmonella spp. in whole liquid eggs, liquid egg white (liquid egg albumen), shell eggs, dried whole eggs, dried egg yolks, and environmental surfaces as stainless steel, plastic, rubber, ceramic tiles, and sealed concrete.
Genus Profundiconus Kuroda, 1956 (Gastropoda, Conoidea): Morphological and molecular studies, with the description of five new species from the Solomon Islands and New Caledonia
Authors: Tenorio Manuel J. , Castelin Magalie
Published: January 2016

The genus Profundiconus Kuroda, 1956 is reviewed. The morphological characters of the shell, radular tooth and internal anatomy of species in Profundiconus are discussed. In particular, we studied Profundiconus material collected by dredging in deep water during different scientific campaigns carried out in the Solomon Islands, Madagascar, Papua New Guinea and New Caledonia. We reconstructed a phylogeny of 55 individuals based on partial mitochondrial cox1 gene sequences. The phylogeny shows several clades containing individuals that do not match any of the known species of Profundiconus based on their shell and radular morphologies, and are introduced here as five new species: Profundiconus maribelae sp. nov. from the Solomon Islands; P. virginiae sp. nov. from Chesterfield Plateau (New Caledonia); P. barazeri sp. nov. from Chesterfield Plateau and the Grand Passage area (New Caledonia); P. puillandrei sp. nov. from Norfolk Ridge (New Caledonia), Kermadec Ridge (New Zealand) and possibly Balut Island (Philippines); and P. neocaledonicus sp. nov. from New Caledonia. Furthermore, Profundiconus teramachii forma neotorquatus (da Motta, 1984) is raised to specific status as P. neotorquatus (da Motta, 1984).
Les mots d’une migration postcoloniale dans les récits de Juifs montréalais
Authors: Cohen Yolande , Messika Martin , Cohen Fournier Sara
Published: January 2016

Au coeur des débats historiographiques et mémoriels sur le départ des Juifs du
Maroc à partir des années 1950, les histoires de vie de migrants installés à Montréal
permettent de jeter un nouvel éclairage sur la perception qu’ont les acteurs des processus
migratoires. Cet article analyse les récits de sept d’entre eux qui, interrogés sur les
circonstances de leur départ, nous ont livré leurs souvenirs, témoignage d’une mémoire
brouillée et entrecoupée de silences. Les auteur.es suggèrent que derrière ces non-dits se
profile par défaut une réitération de l’exode multiséculaire des Juifs, dont l’espace
francophone est devenu l’un des centres de gravité. Cet article est basé sur les résultats
d’une enquête d’histoire orale menée à Montréal entre 2008 et 2012 dans le cadre de la vaste
étude Histoires de vie de Montréal.
Les droits humains, le changement climatique et la billionième tonne
Authors: Shue Henry , Bandini Aude
Published: January 2016

Au vu de l’indolence, voire de l’impavidité dont témoignent les approches qu’ont adoptées la plupart des pays du monde à l’égard du changement climatique, il semble n’y avoir guère d’urgence. La question est de savoir en quoi cela pose problème, si problème il y a. À cela, je réponds que tout, là-dedans, pose problème et, plus précisément, qu’on peut y voir autant une violation des droits fondamentaux que le signe qu’une occasion en or de protéger ces droits a été ratée. Il est, au contraire, urgent d’agir sur deux fronts convergents. Tout d’abord, il faut faire baisser les émissions, nettement et résolument. La concentration de carbone dans l’atmosphère ne cessera pas de croître tant que l’on n’aura pas ramené les émissions à zéro. Ensuite, il faut que l’on développe des technologies utilisant des sources d’énergie alternatives aussi rapidement qu’il est humainement possible de le faire. Parvenue à ce point, l’humanité pourrait se sortir d’affaire, si du moins nous n’avons pas émis la billionième tonne d’ici là.
Registered report: Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET
Authors: Lesnik Jake , Antes Travis , Kim Jeewon , Griner Erin , Pedro Luisa ,   Reproducibility Project: Cancer Biology
Published: January 2016

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (Errington et al., 2014). This Registered Report describes the proposed replication plan of key experiments from “Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET” by Peinado and colleagues, published in Nature Medicine in 2012 (Peinado et al., 2012). The key experiments being replicated are from Figures 4E, as well as Supplementary Figures 1C and 5A. In these experiments, Peinado and colleagues show tumor exosomes enhance metastasis to bones and lungs, which is diminished by reducing Met expression in exosomes (Peinado et al., 2012). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange and the results of the replications will be published in eLife.
TGFβ-dependent expression of PD-1 and PD-L1 controls CD8+ T cell anergy in transplant tolerance
Authors: Baas Marije , Besançon Alix , Goncalves Tania , Valette Fabrice , Yagita Hideo , Sawitzki Birgit , Volk Hans-Dieter , Waeckel-Enée Emmanuelle , Rocha Benedita , Chatenoud Lucienne , You Sylvaine
Published: January 2016

CD8+ T cell anergy is a critical mechanism of peripheral tolerance, poorly investigated in response to immunotherapy. Here, using a pancreatic islet allograft model and CD3 antibody therapy, we showed, by single cell gene profiling, that intragraft CD8+ lymphocytes coexpressing granzyme B and perforin were selectively depleted through the Fas/FasL pathway. This step led to long-standing anergy of the remaining CD8+ T cells marked by the absence of cytotoxic/inflammatory gene expression also confirmed by transcriptome analysis. This sustained unresponsiveness required the presence of the alloantigens. Furthermore, tissue-resident CD8+ lymphocytes produced TGFβ and expressed the inhibitory receptors PD-1 and PD-L1. Blockade of TGFβ downregulated PD-1 and PD-L1 expression and precipitated graft rejection. Neutralizing PD-1, PD-L1 or TGFβRII signaling in T cells also abrogated CD3 antibody-induced tolerance. These studies unravel novel mechanisms underlying CD8+ T cell anergy and reveal a cell intrinsic regulatory link between the TGFβ and the PD-1/PD-L1 pathways.
An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes
Authors: Shafqat-Abbasi Hamdah , Kowalewski Jacob M , Kiss Alexa , Gong Xiaowei , Hernandez-Varas Pablo , Berge Ulrich , Jafari-Mamaghani Mehrdad , Lock John G , Strömblad Staffan
Published: January 2016

Mesenchymal (lamellipodial) migration is heterogeneous, although whether this reflects progressive variability or discrete, 'switchable' migration modalities, remains unclear. We present an analytical toolbox, based on quantitative single-cell imaging data, to interrogate this heterogeneity. Integrating supervised behavioral classification with multivariate analyses of cell motion, membrane dynamics, cell-matrix adhesion status and F-actin organization, this toolbox here enables the detection and characterization of two quantitatively distinct mesenchymal migration modes, termed 'Continuous' and 'Discontinuous'. Quantitative mode comparisons reveal differences in cell motion, spatiotemporal coordination of membrane protrusion/retraction, and how cells within each mode reorganize with changed cell speed. These modes thus represent distinctive migratory strategies. Additional analyses illuminate the macromolecular- and cellular-scale effects of molecular targeting (fibronectin, talin, ROCK), including 'adaptive switching' between Continuous (favored at high adhesion/full contraction) and Discontinuous (low adhesion/inhibited contraction) modes. Overall, this analytical toolbox now facilitates the exploration of both spontaneous and adaptive heterogeneity in mesenchymal migration.
Mutational scanning reveals the determinants of protein insertion and association energetics in the plasma membrane
Authors: Elazar Assaf , Weinstein Jonathan , Biran Ido , Fridman Yearit , Bibi Eitan , Fleishman Sarel Jacob
Published: January 2016

Insertion of helix-forming segments into the membrane and their association determines the structure, function, and expression levels of all plasma membrane proteins. However, systematic and reliable quantification of membrane-protein energetics has been challenging. We developed a deep mutational scanning method to monitor the effects of hundreds of point mutations on helix insertion and self-association within the bacterial inner membrane. The assay quantifies insertion energetics for all natural amino acids at 27 positions across the membrane, revealing that the hydrophobicity of biological membranes is significantly higher than appreciated. We further quantitate the contributions to membrane-protein insertion from positively charged residues at the cytoplasm-membrane interface and reveal large and unanticipated differences among these residues. Finally, we derive comprehensive mutational landscapes in the membrane domains of Glycophorin A and the ErbB2 oncogene, and find that insertion and self-association are strongly coupled in receptor homodimers.
Single-cell analysis of transcription kinetics across the cell cycle
Authors: Skinner Samuel O , Xu Heng , Nagarkar-Jaiswal Sonal , Freire Pablo R , Zwaka Thomas P , Golding Ido
Published: January 2016

Transcription is a highly stochastic process. To infer transcription kinetics for a gene-of-interest, researchers commonly compare the distribution of mRNA copy-number to the prediction of a theoretical model. However, the reliability of this procedure is limited because the measured mRNA numbers represent integration over the mRNA lifetime, contribution from multiple gene copies, and mixing of cells from different cell-cycle phases. We address these limitations by simultaneously quantifying nascent and mature mRNA in individual cells, and incorporating cell-cycle effects in the analysis of mRNA statistics. We demonstrate our approach on Oct4 and Nanog in mouse embryonic stem cells. Both genes follow similar two-state kinetics. However, Nanog exhibits slower ON/OFF switching, resulting in increased cell-to-cell variability in mRNA levels. Early in the cell cycle, the two copies of each gene exhibit independent activity. After gene replication, the probability of each gene copy to be active diminishes, resulting in dosage compensation.
Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove
Authors: McMurtrey Curtis , Trolle Thomas , Sansom Tiffany , Remesh Soumya G , Kaever Thomas , Bardet Wilfried , Jackson Kenneth , McLeod Rima , Sette Alessandro , Nielsen Morten , Zajonc Dirk M , Blader Ira J , Peters Bjoern , Hildebrand William
Published: January 2016

HLA class I presentation of pathogen-derived peptide ligands is essential for CD8+ T-cell recognition of Toxoplasma gondii infected cells. Currently, little data exist pertaining to peptides that are presented after T. gondii infection. Herein we purify HLA-A*02:01 complexes from T. gondii infected cells and characterize the peptide ligands using LCMS. We identify 195 T. gondii encoded ligands originating from both secreted and cytoplasmic proteins. Surprisingly, T. gondii ligands are significantly longer than uninfected host ligands, and these longer pathogen-derived peptides maintain a canonical N-terminal binding core yet exhibit a C-terminal extension of 1–30 amino acids. Structural analysis demonstrates that binding of extended peptides opens the HLA class I F’ pocket, allowing the C-terminal extension to protrude through one end of the binding groove. In summary, we demonstrate that unrealized structural flexibility makes MHC class I receptive to parasite-derived ligands that exhibit unique C-terminal peptide extensions.