Electrical and optical spectroscopy for quantitative screening of hepatic steatosis in donor livers.

Macro-steatosis in deceased donor livers is increasingly prevalent and is associated with poor or non-function of the liver upon reperfusion. Current assessment of the extent of steatosis depends upon the macroscopic assessment of the liver by the surgeon and histological examination, if available. In this paper we demonstrate electrical and optical spectroscopy techniques which quantitatively characterize fatty infiltration in liver tissue. Optical spectroscopy showed a correlation coefficient of 0.85 in humans when referenced to clinical hematoxylin and eosin (H&E) sections in 20 human samples. With further development, an optical probe may provide a comprehensive measure of steatosis across the liver at the time of procurement.

Quantitative approaches for characterising fibrillar protein nanostructures

Polypeptide sequences have an inherent tendency to self-assemble into filamentous nanostructures commonly known as amyloid fibrils. Such self-assembly is used in nature to generate a variety of functional materials ranging from protective coatings in bacteria to catalytic scaffolds in mammals. The aberrant self-assembly of misfolded peptides and proteins is also, however, implicated in a range of disease states including neurodegenerative conditions such as Alzheimer's and Parkinson's diseases. It is increasingly evident that the intrinsic material properties of these structures are crucial for understanding the thermodynamics and kinetics of the pathological deposition of proteins, particularly as the mechanical fragmentation of aggregates enhances the rate of protein deposition by exposing new fibril ends which can promote further growth. We discuss here recent advances in physical techniques that are able to characterise the hierarchical self-assembly of misfolded protein molecnles and define their properties. © 2010 Materials Research Society.

Quantitative RNA-seq analysis of the campylobacter jejuni transcriptome

Campylobacter jejuni is the most common bacterial cause of foodborne disease in the developed world. Its general physiology and biochemistry, as well as the mechanisms enabling it to colonize and cause disease in various hosts, are not well understood, and new approaches are required to understand its basic biology. High-throughput sequencing technologies provide unprecedented opportunities for functional genomic research. Recent studies have shown that direct Illumina sequencing of cDNA (RNA-seq) is a useful technique for the quantitative and qualitative examination of transcriptomes. In this study we report RNA-seq analyses of the transcriptomes of C. jejuni (NCTC11168) and its rpoN mutant. This has allowed the identification of hitherto unknown transcriptional units, and further defines the regulon that is dependent on rpoN for expression. The analysis of the NCTC11168 transcriptome was supplemented by additional proteomic analysis using liquid chromatography-MS. The transcriptomic and proteomic datasets represent an important resource for the Campylobacter research community. © 2011 SGM.

A quantitative survey of the benthic infauna of northern Monterey Bay, California: Annual report, Part 8, 1973

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Reducing non-point DOC and nitrogen exports from rice fields: A pilot study and quantitative survey to determine the effects of different hydrologic management practices : Deliverable 15.3 Final Report

Rice cultivation at any level in the Sacramento–San Joaquin Delta (existing or expanded) compels the need to quantify surface and subsurface loads of dissolved organic carbon (DOC), disinfection byproduct precursors (DBPPs) and nitrogen. This information can be used to develop Best Management Practices (BMPs) to reduce export of these constituents in order to improve drinking water quality. Although rice cultivation in the Delta is relatively limited, several factors outside of this research could contribute to increased rice acreage in the Delta: • Recently developed rice varieties seem more suitable for the Delta climate than earlier varieties which required warmer conditions; • Previous economic analyses (Appendix A.10) suggest rice is more profitable than corn, a dominant land use in the Delta; • Recent studies on wetlands at Twitchell Island suggest rice production can help mitigate oxidative subsidence (Miller et al. 2000); • The different oxidative states that result from flooding in rice as compared to those found in crops that require drained soils may help control crop specific weeds and nematodes when rice is incorporated into a crop rotation; and • Providing flooded conditions during a greater part of the year than other crops may benefit water birds. ... (PDF contains 249 pages)

Digging into signs: Developing standard annotation practices for cross-linguistic, quantitative analysis of sign language data. Final Report.

For sign languages used by deaf communities, linguistic corpora have until recently been unavailable, due to the lack of a writing system and a written culture in these communities, and the very recent advent of digital video. Recent improvements in video and computer technology have now made larger sign language datasets possible; however, large sign language datasets that are fully machine-readable are still elusive. This is due to two challenges. 1. Inconsistencies that arise when signs are annotated by means of spoken/written language. 2. The fact that many parts of signed interaction are not necessarily fully composed of lexical signs (equivalent of words), instead consisting of constructions that are less conventionalised. As sign language corpus building progresses, the potential for some standards in annotation is beginning to emerge. But before this project, there were no attempts to standardise these practices across corpora, which is required to be able to compare data crosslinguistically. This project thus had the following aims: 1. To develop annotation standards for glosses (lexical/word level) 2. To test their reliability and validity 3. To improve current software tools that facilitate a reliable workflow Overall the project aimed not only to set a standard for the whole field of sign language studies throughout the world but also to make significant advances toward two of the world’s largest machine-readable datasets for sign languages – specifically the BSL Corpus (British Sign Language, http://bslcorpusproject.org) and the Corpus NGT (Sign Language of the Netherlands, http://www.ru.nl/corpusngt).

Quantitative composition and distribution of the macrobenthic invertebrate fauna of the Continental Shelf ecosystems of the Northeastern United States

From the mid-1950's to the mid-1960's a series of quantitative surveys of the macrobenthic invertebrate fauna were conducted in the offshore New England region (Maine to Long Island, New York). The surveys were designed to 1) obtain measures of macrobenthic standing crop expressed in terms of density and biomass; 2) determine the taxonomic composition of the fauna (ca. 567 species); 3) map the general features of macrobenthic distribution; and 4) evaluate the fauna's relationships to water depth, bottom type, temperature range, and sediment organic carbon content. A total of 1,076 samples, ranging from 3 to 3,974 m in depth, were obtained and analyzed. The aggregate macrobenthic fauna consists of 44 major taxonomic groups (phyla, classes, orders). A striking fact is that only five of those groups (belonging to four phyla) account for over 80% of both total biomass and number of individuals of the macrobenthos. The five dominant groups are Bivalvia, Annelida, Amphipoda, Echninoidea, and Holothuroidea. Other salient features pertaining to the macrobenthos of the region are the following: substantial differences in quantity exist among different geographic subareas within the region, but with a general trend that both density and biomass increase from northeast to southwest; both density and biomass decrease with increasing depth; the composition of the bottom sediments significantly influences both the kind and quantity of macrobenthic invertebrates, the largest quantities of both measures of abundance occurring in the coarser grained sediments and diminishing with decreasing particle size; areas with marked seasonal changes in water temperature support an abundant and diverse fauna, whereas a uniform temperature regime is associated with a sparse, less diverse fauna; and no detectable trends are evident in the quantitative composition of the macrobenthos in relation to sediment organic carbon content. (PDF file contains 246 pages.)

A quantitative analysis of the phytoplankton of the Gulf of Panama: I. Results of the regional phytoplankton surveys during July and November 1957 and March 1958

ENGLISH: 1. Quantitative phytoplankton samples were collected by the Inter-American Tropical Tuna Commission at the surface and ten meters in the Gulf of Panama, as follows: a) 18-21 March, 1958 (31 stations)-during the height of the upwelling season, b) 10-12 July, 1957 (10 stations)-during the transition to the rainy season at a time when mild upwelling winds reappear, c) 7-8 November, 1957 (15 stations)-during the height of the rainy season. 2. Maximum phytoplankton populations occurred during the upwelling season, followed by a considerable decline during July, and a further Subsidence during November. 3. A remarkable regional uniformity in species composition was observed during the surveys despite regional differences in growth conditions. Diatoms overwhelmingly dominated the communities. 4. During all surveys, the innermost regions, generally north of 8°30'N, were the most productive. The least productive areas were in the offing of San Miguel Bay and Parita Bay, suggesting that nutrient accretion via runoff is inadequate to sustain sizeable autotrophic plant populations in those regions. 5. During all surveys, phytoplankton growth appeared to be limited by nutrient availability. 6. During all surveys, phytoplankton growth appeared to be related to depth of the water column. 7. Although below average rainfall contributed to unusually favorable growth conditions (reduced stability, increased transparency and, presumably, nutrient reserves) during the November survey relative to November 1955 and 1956 at 8°45'N, 79°23'W, the anticipated heightened phytoplankton response was not observed. 8. During the November survey, the local diatom responses and their regional fluctuations could be satisfactorily related to the accompanying surface salinity conditions. However, this correspondence is undoubtedly attributable to factors associated with the observed salinity levels, probably nutrients, rather than salinity directly. 9. Unusually warm conditions occurred during the March survey, attributable to considerably weaker upwelling winds than normally occurring then, which contributed to a considerably lower standing crop and a retardation in succession of three to five weeks relative to that observed during 1955-1957 at 8°45'N, 79°23'W in the Gulf of Panama. 10. During the March survey, a well defined inverse relationship existed between mean temperature and mean diatom abundance in the upper ten meters, and between transparency and mean diatom abundance. A direct relationship occurred between surface salinity and mean diatom abundance in the upper ten meters. These relationships are interpreted to indicate that diatom abundance primarily reflected the nutrient concentrations associated with a given upwelling intensity, rather than describing casual relationships. 11. The survey results indicate that the phytoplankton dynamics observed at 8°45'N, 79°23'W from November, 1954 through May, 1957 are generally representative of the Gulf of Panama. 12. The following new forms, to be described in a later publication, were observed during the surveys: Actinoptychus undulatus f. catenata n.f., Asterionella japonica f. tropicum n.f., Leptocylindrus maximus n. sp., Skeletonema costatum f. tropicum n.f. SPANISH: 1. La Comisión Interamericana del Atun Tropical recolectó en el Golfo de Panama muestras cuantitativas de fitoplancton en la superficie y a los diez metros, como sigue: a) Del 18 al 21 de marzo de 1958 (31 estaciones)-durante el maximum de la estación de afloramiento. b) Del 10 al 12 de julio de 1957 (10 estaciones)-durante la epóca de transición a la estación lluviosa cuando reaparecen los vientos ligeros que causan el afloramiento. c) Del 7 al 8 de noviembre de 1957 (15 estaciones)-durante el maximum de la estación lluviosa. 2. Las poblaciones maximas de fitoplancton aparecieron durante la estación de afloramiento, seguido por una considerable disminución durante el mes de julio y una calma durante noviembre. 3. Durante la investigación se observó una remarcable uniformidad regional en la composición de las especies a pesar de las diferencias regionales en las condiciones de crecimiento. Las diatomeas predominaban en gran numero en las comunidades. 4. Durante todas las investigaciones, las regiones mas cerca de la costa, generalmente al norte de los 8°30'N, eran las mas productivas. Las areas menos productivas fueron las mar afuera de las Bahias de San Miguel y Parita, lo que sugiere que el aumento en las sales nutritivas causado por las escorrentias es inadecuado para sostener poblaciones grandes de plantas autotróficas en estas regiones. 5. Durante todas las investigaciones, el crecimiento del fitoplancton parecio estar limitado por la disponibilidad de las. sales nutritivas. 6. Durante todas las investigaciones el crecimiento del fitoplancton parecio estar relacionado con la profundidad de la columna de agua. 7. Aunque las precipitacion por debajo del promedio normal contribuyo a condiciones desusadamente favorables de crecimiento (estabilidad reducida, aumento de la transparencia y, presumiblemente, de la reserva de sales nutritivas) durante la investigación de noviembre en relación a noviembre de 1955 y de 1956 en los 8°45'N, 79°23'W, no se observo-la alta reacción de fitoplancton que se esperaba. 8. Durante la investigación de noviembre, las reacciones locales de las diatomeas y sus fluctuaciones regionales pudieron relacionarse en forma satisfactoria con condiciones asociadas con la salinidad de la superficie. Sin embargo, esta correspondencia puede atribuirse sin duda a factores asociados con los niveles observados de salinidad, probablemente con las sales nutritivas, en lugar de directamente con la salinidad. 9. Condiciones calurosas no comunes ocurrieron durante la investigación de marzo, las que pueden atribuirse a que los vientos que ocasionan el afloramiento fueran mas debiles que los normales, lo que contribuyó a que la cosecha estable fuera considerablemente mas baja y a la demora de tres a cinco semanas en la sucecion relativa a la que se observó durante 1955-1957 en los 8°45'N, 8°23'W, en el Golfo de Panama. 10. Durante la investigación de marzo, existió una relación inversa bien definida entre la temperatura y la abundancia media de las diatomeas en los diez metros superiores, y entre la transparencia y la abundancia media de las diatomeas. Una relación directa ocurrio entre la salinidad de superficie y la abundancia media de las diatomeas en los diez metros superiores. Estas relaciones se interpretan como indicadoras de que la abundancia de diatomeas refleja primeramente las concentraciones de las sales nutritivas asociadas con una intensidad de afloramiento dada, en lugar de describir relaciones causales. 11. Los resultados de la investigacion indican que la dinamica del fitoplancton observada en los 8°45'N, 79°23'W, desde noviembre de 1954 a mayo de 1957, es generalmente representativa del Golfo de Panama. 12. Durante las investigaciones se observaron las siguientes formas nuevas, las que seran descritas en una publicación posterior: Actinoptychus undulatus f. catenata n.f., Asterionella japonica f. tropicum n.f., Leptocylindrus maximus n. sp., Skeletonema costatum f. tropicum n.f.

A quantitative witness for Greenberger-Horne-Zeilinger entanglement

Along with the vast progress in experimental quantum technologies there is an increasing demand for the quantification of entanglement between three or more quantum systems. Theory still does not provide adequate tools for this purpose. The objective is, besides the quest for exact results, to develop operational methods that allow for efficient entanglement quantification. Here we put forward an analytical approach that serves both these goals. We provide a simple procedure to quantify Greenberger-Horne-Zeilinger-type multipartite entanglement in arbitrary three-qubit states. For two qubits this method is equivalent to Wootters' seminal result for the concurrence. It establishes a close link between entanglement quantification and entanglement detection by witnesses, and can be generalised both to higher dimensions and to more than three parties.

A quantitative analysis of the phytoplankton of the Gulf of Panama II. On the relationship between C14 assimilation and the diatom standing crop

ENGLISH: The Inter-American Tropical Tuna Commission has maintained a hydro-biological station in the Gulf of Panama located at 8°45'N, 79°23'W in connection with their ecological investigation of the anchoveta (Cetengraulis mysticetus), a tuna baitfish (see Peterson, 1961, for references) . The depth is approximately 42 meters at mean low water at this station. Routine hydrographic and biological observations have been made (Schaefer, Bishop and Howard, 1958; Schaefer and Bishop, 1958; Forsbergh, 1963), including the collection of quantitative phytoplankton samples from November 1954 through May 1957 (Smayda, 1959; unpublished). The seasonal and regional variations in phytoplankton growth in the Gulf of Panama have also been investigated (Smayda, 1963). The relationships existing between C1 4 assimilation as determined by 24 hour in situ experiments and diatom standing crop at 10 meters when expressed as cell numbers, cell volume, cell surface area and cell plasma volume have been assessed for 30 observations made between November 1954 and May 1957 at 8°45'N, 79°23'W. The average cell volume and cell surface area characteristics for 110 diatom species and varieties are presented. SPANISH: Las relaciones existentes entre la asimilación del C14 , determinadas después de 24 horas de experimentos in situ, y la cosecha estable de las diatomeas a 10 metros, expresando el número de células, volumen celular, área de la superficie celular y volumen del plasma celular, han sido determinadas por medio de 30 observaciones hechas entre noviembre de 1954 y mayo de 1957, a los 8°45'N, 79°23'W. Se presenta, para 110 especies y variedades de diatomeas, el promedio de las características del volumen celular y del área de la superficie celular. (PDF contains 67 pages.)

A quantitative analysis of the phytoplankton of the Gulf of Panama III. General ecological conditions and the phytoplankton dynamics at 8°45'N, 79°23'W from November 1954 to May 1957

Bi-weekly phytoplankton samples were collected at 0, 10, and 20 m and enumerated by the Utermöhl sedimentation technique; 14C productivity measurements at 10 m, oblique zooplankton tows, and routine hydrographic observations were also made. Northerly winds induce upwelling during December-April, followed by a rainy season; a slight resurgence in upwelling may occur during July and/or August. Annual variations in upwelling intensity and rainfall occur. During upwelling, the upper 50 m, about 30 per cent of the total volume of the Gulf of Panama, is replaced with water 5 to 10 C colder than the more stratified, turbid and nutrient impoverished watermass present during the rainy season. The mean annual runoff accompanying an average annual precipitation of 2731 mm is estimated to equal a layer of fresh water 3.2 m thick. About 10 per cent of the phytoplankton phosphate and inorganic nitrogen requirements during the rainy season are accreted. (PDF contains 260 pages.)

Cost effectiveness of a combination of instruments for global warming: a quantitative approach for Spain

Climate change is an important environmental problem and one whose economic implications are many and varied. This paper starts with the presumption that mitigation of greenhouse gases is a necessary policy that has to be designed in a cost effective way. It is well known that market instruments are the best option for cost effectiveness. But the discussion regarding which of the various market instruments should be used, how they may interact and what combinations of policies should be implemented is still open and very lively. In this paper we propose a combination of instruments: the marketable emission permits already in place in Europe for major economic sectors and a CO(2) tax for economic sectors not included in the emissions permit scheme. The study uses an applied general equilibrium model for the Spanish economy to compute the results obtained with the new mix of instruments proposed. As the combination of the market for emission permits and the CO(2) tax admits different possibilities that depend on how the mitigation is distributed among the economic sectors, we concentrate on four possibilities: cost-effective, equalitarian, proportional to emissions, and proportional to output distributions. Other alternatives to the CO(2) tax are also analysed (tax on energy, on oil and on electricity). Our findings suggest that careful, well designed policies are needed as any deviation imposes significant additional costs that increase more than proportionally to the level of emissions reduction targeted by the EU.