Digital image treatment applied to ichnological analysis of marine core sediments

Characterization of trace fossils in marine core sediments is, most times, difficult due to the weak differentiation between biogenic structures and the host sediment, especially in pelagic and hemipelagic facies. This problem is accentuated where a high degree of bioturbation is associated with composite ichnofabrics. Simple methods are presented here based on modifications to image features such as contrast, brightness, vibrance, saturation, exposure, lightness, and color balance using the software Adobe Photoshop CS6 (Adobe Systems, San Jose, CA, USA) to enhance visibility and thus allow for a better identification of the trace fossils. Adjustments involving brightness, levels and vibrance generally give better results. This approach was applied to marine cores of pelagic and hemipelagic sediments obtained from the Integrated Ocean Drilling Program Expedition 339, Site U1385. Enhancing the digital images facilitates ichnological analysis through improving the visibility of weakly observed trace fossils, and in some cases revealing traces not detected previously.     

Quantitative immunoelectrophoretic methods applied to the immunochemistry of Candida

Cytoplasmic soluble extracts of yeasts were compared by quantitative immunoelectrophoretic methods. Comparative studies of Candida albicans and Candida tropicalis permitted to confirm the antigenic complexity of fungi and the existence of important cross-reacting antigens between this two yeast, to demonstrate the specificity of the Candida tropicalis cell-wall antiserum and the presence of soluble cell-wall constituents in cytoplasmic yeast extracts. Crossed-line immunoelectrophoresis with and without absorption of antibodies in situ demonstrated four specific antigens unique to Candida albicans group A cytoplasmic extract not shared with the group B. The other procedures used were not sufficient for identification, since the resulting patterns were confusingly complex.     

Parasitism,the diversity of life,and paleoparasitology

The parasite-host-environment system is dynamic, with several points of equilibrium. This makes it difficult to trace the thresholds between benefit and damage, and therefore, the definitions of commensalism, mutualism, and symbiosis become worthless. Therefore, the same concept of parasitism may encompass commensalism, mutualism, and symbiosis. Parasitism is essential for life. Life emerged as a consequence of parasitism at the molecular level, and intracellular parasitism created evolutive events that allowed species to diversify. An ecological and evolutive approach to the study of parasitism is presented here. Studies of the origin and evolution of parasitism have new perspectives with the development of molecular paleoparasitology, by which ancient parasite and host genomes can be recovered from disappeared populations. Molecular paleoparasitology points to host-parasite co-evolutive mechanisms of evolution traceable through genome retrospective studies.     

Estimating the age structure of a buried adult population: A new statistical approach applied to archaeological digs in France

Paleodemographers have developed several methods for estimating the age structure of historical populations in absence of civil registration data. Starting from biological indicators alone, they use a reference population of known sex and age to assess the conditional distribution of the biological indicator given age. However, the small amount of data available and the unstable nature of the related statistical problem mean that most methods are disappointing. Using the most reliable reference data possible, we propose a simple statistical method, integrating the maximum amount of information included in the actual data, which quite significantly improves age estimates for a buried population. Here the method is applied to a French cemetery used from Late Antiquity to the end of the Early Middle Ages. Am J Phys Anthropol, 2013. © 2012 Wiley Periodicals, Inc.     

Helminths as heirlooms and souvenirs: a review of new world paleoparasitology

Evidence from studies on ancient human feces, intestinal contents and organs of preserved bodies has established that Enterobius vermicularis, Trichuris trichiura, Diphyllobothrium spp and probably Trichinella spiralis infected humans in the pre-Columbian New World. These species, and perhaps other common human helminths for which there is not yet convincing evidence, probably accompanied transberingeal immigrants and their dogs, and thus can be seen as heirloom parasites. Early humans on the American continents were affected by helminths of native animals such as Paragonimus and Cryptocotyle, and these have also been found in precontact human remains. Michael Kliks considers that the indigenous parasites infecting early Americans may be viewed as zoonotic souvenirs of some 50 millennia of migrations from Alaska to Patagonia. Among the most serious zoonoses would have been infection by cystic hydatid larvae of echinococcid tapeworms, the many enzootic filarial worms, and a variety of larval trematodes and nematodes.     

Historical biogeography of olive domestication (Olea europaea L.) as revealed by geometrical morphometry applied to biological and archaeological material

Aim This study intends to improve our understanding of historical biogeography of olive domestication in the Mediterranean Basin, particularly in the north-western area. Location Investigations were performed simultaneously on olive stones from extant wild populations, extant cultivated varieties from various Mediterranean countries, and archaeological assemblages of Spanish, French and Italian settlements. Methods A combination of morphometrics (traditional and geometrical) allowed us to study both the size and shape of endocarp structure. Concerning shape, a size-standardized method coupled with fitted polynomial regression analysis was performed. Results We found morphological criteria for discriminating between wild and cultivated olive cultivars, and established patterns of morphological variation of olive material according to the geographical origin (for extant material) and to the age of the olive forms (for archaeological material). Levels of morphological convergences and divergences between wild olive populations and cultivated varieties are presented as evidence. Main conclusions Morphological changes of endocarps of olive under domestication at both geographical and chronological scales provide new criteria for the identification of olive cultivars. They allow to determine the origins of cultivated forms created and/or introduced in the north-western Mediterranean regions and to understand how human migrations affected the rest of the Western Mediterranean regions. A model of diffusion of olive cultivation is proposed. It shows evidence of an indigenous origin of the domestication process, which is currently recognized in the north-western area since the Bronze Age.     

Destructive and non-destructive microanalysis of biocarbonates applied to anomalous otoliths of archaeological and modern sciaenids (Teleostei) from Peru and Chile

Anomalous otoliths were discovered among modern and archaeological (8th millennium BP) sciaenids. The two species concerned, Cilus gilberti and Sciaena deliciosa, are common on the Peruvian-Chilean coast and do not seem to be affected by this morphological anomaly that maintained in their populations for thousands of years. The carbonates of the anomalous forms, determined by X-ray diffraction, are different from that of the normal otoliths, i.e. calcite and vaterite instead of aragonite. A method of non-destructive analysis by cathodoluminescence is tested and assumptions on the origin of the anomaly and its possible implications on environmental studies are advanced.     

Quantitative models of the rat pulmonary arterial tree morphometry applied to hypoxia-induced arterial remodeling.

Little is known about the constituent hemodynamic consequences of structural changes that occur in the pulmonary arteries during the onset and progression of pulmonary arterial remodeling. Many disease processes are known to be responsible for vascular remodeling that leads to pulmonary arterial hypertension, cor pulmonale, and death. Histology has been the primary tool for evaluating pulmonary remodeling, but it does not provide information on intact vascular structure or the vessel mechanical properties. This study is an extension of our previous work in which we developed an alternative imaging technique to evaluate pulmonary arterial structure. The lungs from Sprague-Dawley rats were removed, perfusion analysis was performed on the isolated lungs, and then an X-ray contrast agent was used to fill the arterial network for imaging. The lungs were scanned over a range of intravascular pressures by volumetric micro-computed tomography, and the arterial morphometry was mapped and measured in the reconstructed isotropic volumes. A quantitative assessment of hemodynamic, structural, and biomechanical differences between rats exposed for 21 days to hypoxia (10% O(2)) or normoxia (21.0% O(2)) was performed. One metric, the normalized distensibility of the arteries, is significantly (P < 0.001) larger [0.025 +/- 0.0011 (SE) mmHg(-1)] (n = 9) in normoxic rats compared with hypoxic [0.015 +/- 0.00077 (SE) mmHg(-1)] (n = 9). The results of the study show that these models can be applied to the Sprague-Dawley rat data and, specifically, can be used to differentiate between the hypoxic and the control groups.     

Quantitative PCR detection of Batrachochytrium dendrobatidis DNA from sediments and water

The fungal pathogen Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis, a disease implicated in amphibian declines on 5 continents. Polymerase chain reaction (PCR) primer sets exist with which amphibians can be tested for this disease, and advances in sampling techniques allow non-invasive testing of animals. We developed filtering and PCR based quantitative methods by modifying existing PCR assays to detect Bd DNA in water and sediments, without the need for testing amphibians; we tested the methods at 4 field sites. The SYBR based assay using Boyle primers (SYBR/Boyle assay) and the Taqman based assay using Wood primers performed similarly with samples generated in the laboratory (Bd spiked filters), but the SYBR/Boyle assay detected Bd DNA in more field samples. We detected Bd DNA in water from 3 of 4 sites tested, including one pond historically negative for chytridiomycosis. Zoospore equivalents in sampled water ranged from 19 to 454 1(-1) (nominal detection limit is 10 DNA copies, or about 0.06 zoospore). We did not detect DNA of Bd from sediments collected at any sites. Our filtering and amplification methods provide a new tool to investigate critical aspects of Bd in the environment.     

Quantitative systematic review of topically applied non-steroidal anti-inflammatory drugs.

OBJECTIVE: To review the effectiveness and safety of topical non-steroidal anti-inflammatory drugs in acute and chronic pain conditions. DESIGN: Quantitative systematic review of randomised controlled trials. DATA SOURCES: 86 trials involving 10,160 patients. MAIN OUTCOME MEASURES: Measures of treatment success approximating at least 50% reduction in pain, local and systemic adverse effects. Analysis at 1 week for acute and 2 weeks for chronic conditions with relative benefit and number needed to treat. RESULTS: In acute pain conditions (soft tissue trauma, strains, and sprains) placebo controlled trials had a relative benefit of 1.7 (1.5 to 1.9), the number needed to treat was 3.9 (3.4 to 4.4). With analysis by drug (at least three trials), ketoprofen (number needed to treat 2.6), felbinac (3.0), ibuprofen (3.5), and piroxicam (4.2) had significant efficacy. Benzydamine and indomethacin were no different from placebo. In chronic pain conditions (osteoarthritis, tendinitis) placebo controlled trials had a relative benefit of 2.0 (1.5 to 2.7); the number needed to treat was 3.1 (2.7 to 3.8). Small trials (< 40 treated patients) exaggerated effectiveness of topical non-steroidals by 33% in acute conditions but not in chronic conditions. There was no relation between trial quality and treatment effect. In both acute and chronic pain local and systemic adverse events and withdrawal from the study related to the drug had a low incidence and were no different from placebo. CONCLUSION: Topical non-steroidal anti-inflammatory drugs are effective in relieving pain in acute and chronic conditions.     

Quantitative estimation of pituitary gonadotropin in juvenile rainbow trout with scanning cytophotometry applied to immunocytochemical preparations

A densitometrical method with computer-controlled scanning cytophotometry has been developed to quantify the amount of gonadotropin (GTH) in immunocytochemically treated paraffin sections of pituitaries of juvenile rainbow trout. Results obtained with this method totally correspond with those established with a radioimmunoassay of pooled pituitaries. Scanningcytophotometry offers the advantage that GTH-content of individual pituitaries of juvenile or small adult fish can be investigated.     

Quantitative tools for comparing animal communication systems: information theory applied to bottlenose dolphin whistle repertoires

Comparative analysis of nonhuman animal communication systems and their complexity, particularly in comparison to human language, has been generally hampered by both a lack of sufficiently extensive data sets and appropriate analytic tools. Information theory measures provide an important quantitative tool for examining and comparing communication systems across species. In this paper we use the original application of information theory, that of statistical examination of a communication system's structure and organization. As an example of the utility of information theory to the analysis of animal communication systems, we applied a series of information theory statistics to a statistically categorized set of bottlenose dolphin Tursiops truncatus, whistle vocalizations. First, we use the first-order entropic relation in a Zipf-type diagram (Zipf 1949 Human Behavior and the Principle of Least Effort) to illustrate the application of temporal statistics as comparative indicators of repertoire complexity, and as possible predictive indicators of acquisition/learning in animal vocal repertoires. Second, we illustrate the need for more extensive temporal data sets when examining the higher entropic orders, indicative of higher levels of internal informational structure, of such vocalizations, which could begin to allow the statistical reconstruction of repertoire organization. Third, we propose using 'communication capacity' as a measure of the degree of temporal structure and complexity of statistical correlation, represented by the values of entropic order, as an objective tool for interspecies comparison of communication complexity. In doing so, we introduce a new comparative measure, the slope of Shannon entropies, and illustrate how it potentially can be used to compare the organizational complexity of vocal repertoires across a diversity of species. Finally, we illustrate the nature and predictive application of these higher-order entropies using a preliminary sample of dolphin whistle vocalizations. The purpose of this preliminary report is to re-examine the original application of information theory to the field of animal communication, illustrate its potential utility as a comparative tool for examining the internal informational structure of animal vocal repertoires and their development, and discuss its relationship to behavioural ecology and evolutionary theory. Copyright 1999 The Association for the Study of Animal Behaviour.     

Recovery techniques for waterlogged archaeological sediments: a comparison of different treatment methods for samples from Neolithic lake shore settlements

This paper presents the first comparable overview of different recovery techniques used for waterlogged Neolithic sediments in the surroundings of the Alps in the last decades. Such an investigation became necessary because it was not known which parts of plants and types of remains were absent or completely underrepresented due to inappropriate recovery techniques in Slovenian archaeobotany up to 2006. During the 2007 excavation of the approximately 5,200 years old Neolithic pile dwelling site of Stare gmajne, Ljubljansko barje, Slovenia, we compared three methods for the investigation of botanical macroremains: method 1 (M1) included rough wet-sieving and subsequent drying of the fractions; method 2 (M2) rough wet sieving and keeping the fractions wet; and method 3 (M3) washing over and keeping the fractions wet. M3 with gentle washing, systematic subsampling, examination, and sorting of macroremains while wet, as well as using 0.355 mm as the smallest sieve mesh size gave the best results. When using the cruder M2 or M1 methods, waterlogged uncarbonized seeds of taxa such as Linum usitatissimum, Papaver somniferum and Brassica rapa, waterlogged chaff of Cerealia and pericarps of Maloideae and Quercus sp., which are all fragile, were underrepresented or even completely absent and therefore the plant spectra were strongly biased. On the contrary, taxa with lignified seed/fruit walls like Cornus mas, Corylus avellana or Rubus sp. were overrepresented when using the M2 and particularly the M1 method. The application of the M3, instead of the M1 method which has been traditionally used in Slovenian archaeobotany, helped us to identify uncarbonized remains of Linum usitatissimum and various species of Triticum for the first time in a waterlogged Neolithic site in Slovenia. Our study should contribute to a standardization of methods, which is desperately needed in archaeobotany. The study clearly shows that the plant spectra can be strongly biased if inappropriate handling techniques are used. The conclusions hold for all kinds of waterlogged sediments of different periods.     

Quantitative microbiological risk assessment: principles applied to determining the comparative risk of salmonellosis from chicken products

Since causal links have been established between food-borne illness and particular microorganisms, it has been possible to assess the public health risks of their presence in foods and propose measures to ensure the safety of customers. Effective control measures for food safety have been based on knowledge of the resistance of pathogenic microorganisms to the treatments used for preservation (e.g. acidification or reduced water activity) or decontamination (e.g. pasteurisation or sterilisation). Using this principle, food safety has been managed informally and successfully within the food industry for many years. Recently, formal risk assessment schemes, for example from Codex Alimentarius, have developed and placed the elements of decision-making on suitable control measures into a formal framework with clearly identifiable stages. The output of the four stages of a formal risk assessment (hazard identification, hazard characterisation, exposure assessment and risk characterisation) provides the basis for decisions on actions needed to control the identified hazard. There are many difficulties in ensuring that risk assessments are realistic and accessible to potential users, in many cases their value is limited by the data available. The study reported here on control of Salmonella in poultry products illustrates that it is possible to produce a comparative risk assessment based on published data. This study is not a full quantitative risk assessment, but provide useful pointers for a risk manager. Differences are discussed between the exposure assessment data needed to propose controls for infectious or toxigenic pathogens. For infectious pathogens, the presence of viable and infectious microorganisms is itself the hazard, but for toxigenic microorganisms, absence or destruction of viable cells at ingestion does not in itself ensure the absence of toxin. For toxin hazards, exposure assessment needs to consider previous conditions that may have led to toxin formation and persistence, rather than just the level of microbes at ingestion.     

Quantitative analytical technique applied to histopathology of birds infected experimentally by the virus of chicken anemia virus

This research was conducted on ten glass slides selected from the histopathology evaluation chickens. Five slides of control's chickens healthy and five slides of chickens infected experimentally with chicken anemia virus (CAV slide) between one and twenty-one days post infection (PI), they were analyzed in magnifications of 200x and 400x. Histopathology showed severe bone marrow hypoplasia to complete aplasia, fully depletion of the erythrocytic and granulocytic series, both accompanied by space occupying adipocytic replacement. Foci of erythropoietic hyperplasia with intense mielopoietic activity, some hemocytoblast increased of size, with large nucleus. A quantitative analytical technique by Positive Pixel Count Algorithm was applied. It demonstrated that measures area stained of control slides were higher than CAV slides (Average: 61% vs. 25%, respectively). So, the control slides showed strong positivity, due to the presence of bigger quantity of cells of erythrocytic and granulocytic series. The CAV slides of seven days PI had high positivity (average: 94%), it was explained because the chicken anemia virus takes place severe lesions between ten to seventeen days PI, after 21 days PI the cellular regeneration is observed that is evidenced by means of focuses of erythroblastoid cells hyperplasia. This technique demonstrates in a quantitative way the severe decrease of the cellular components of the bone marrow in presence of the infection for CAV, supporting with numeric data the histology image evaluated by the pathologist. Therefore, it can be used as support to the histopathology of field samples to evaluate the presence of lesions taken place by CAV and this way to improve the quality and efficiency of the veterinary pathology services.