Spatial effects in real networks: measures, null models, and applications

Spatially embedded networks are shaped by a combination of purely topological (space-independent) and space-dependent formation rules. While it is quite easy to artificially generate networks where the relative importance of these two factors can be varied arbitrarily, it is much more difficult to disentangle these two architectural effects in real networks. Here we propose a solution to the problem by introducing global and local measures of spatial effects that, through a comparison with adequate null models, effectively filter out the spurious contribution of non-spatial constraints. Our filtering allows us to consistently compare different embedded networks or different historical snapshots of the same network. As a challenging application we analyse the World Trade Web, whose topology is expected to depend on geographic distances but is also strongly determined by non-spatial constraints (degree sequence or GDP). Remarkably, we are able to detect weak but significant spatial effects both locally and globally in the network, showing that our method succeeds in retrieving spatial information even when non-spatial factors dominate. We finally relate our results to the economic literature on gravity models and trade globalization

A comparison of certain extracting agents for extraction of adenosine triphosphate (ATP) from microorganisms for use in the firefly luciferase ATP assay

Firefly luciferase ATP assay is used in clinical and industrial applications, such as determination of urinary infection levels, microbial susceptibility testing, and monitoring of yeast levels in beverages. Three categories of extractants were investigated for their extracting efficiency. They were ionizing organic solvents, nonionizing organic solvents, and inorganic acids. Dimethylsulfoxide and formamide represented the ionizing organic solvents, while n-butanol, chloroform, ethanol, acetone, and methylene chloride were used for the nonionizing organic solvents. Nitric acid and perchloric acid were chosen for the inorganic acids category. Pathogens were tested with each solvent. They included: Saccharomyces carlsbergensis, E. coli, Staphylococcus aureus, Klebsiella pneumoniae, Enterobacter species, Proteus mirabilis, Proteus vulgaris, Staphylococcus epidermidis, Streptococcus faecalis, Pseudomonas aeruginosa, and Candida albicans. These results are shown in graphic representations

Problem areas in the use of the firefly luciferase assay for bacterial detection

By purifying the firefly luciferase extract and adding all necessary chemicals but ATP in excess, an assay for ATP was performed by measuring the amount of light produced when a sample containing soluble ATP is added to the luciferase reaction mixture. Instrumentation, applications, and basic characteristics of the luciferase assay are presented. Effect of the growth medium and length of time grown in this medium on ATP per viable E. coli values is shown in graphic form, along with an ATP concentration curve showing relative light units versus ATP injected. Reagent functions and concentration methods are explored. Efforts to develop a fast automatable system to detect the presence of bacteria in biological fluids, especially urine, resulted in the optimization of procedures for use with different types of samples

Rapid method for determination of antimicrobial susceptibilities pattern of urinary bacteria

Method determines bacterial sensitivity to antimicrobial agents by measuring level of adenosine triphosphate remaining in the bacteria. Light emitted during reaction of sample with a mixture of luciferase and luciferin is measured

Application of luciferase assay for ATP to antimicrobial drug susceptibility

The susceptibility of bacteria, particularly those derived from body fluids, to antimicrobial agents is determined in terms of an ATP index measured by culturing a bacterium in a growth medium. The amount of ATP is assayed in a sample of the cultured bacterium by measuring the amount of luminescent light emitted when the bacterial ATP is reacted with a luciferase-luciferin mixture. The sample of the cultured bacterium is subjected to an antibiotic agent. The amount of bacterial adenosine triphosphate is assayed after treatment with the antibiotic by measuring the luminescent light resulting from the reaction. The ATP index is determined from the values obtained from the assay procedures

Laboratory procedures manual for the firefly luciferase assay for adenosine triphosphate (ATP)

A manual on the procedures and instruments developed for the adenosine triphosphate (ATP) luciferase assay is presented. Data cover, laboratory maintenance, maintenance of bacterial cultures, bacteria measurement, reagents, luciferase procedures, and determination of microbal susceptibility to antibiotics

Reconciling long-term cultural diversity and short-term collective social behavior

An outstanding open problem is whether collective social phenomena occurring over short timescales can systematically reduce cultural heterogeneity in the long run, and whether offline and online human interactions contribute differently to the process. Theoretical models suggest that short-term collective behavior and long-term cultural diversity are mutually excluding, since they require very different levels of social influence. The latter jointly depends on two factors: the topology of the underlying social network and the overlap between individuals in multidimensional cultural space. However, while the empirical properties of social networks are well understood, little is known about the large-scale organization of real societies in cultural space, so that random input specifications are necessarily used in models. Here we use a large dataset to perform a high-dimensional analysis of the scientific beliefs of thousands of Europeans. We find that inter-opinion correlations determine a nontrivial ultrametric hierarchy of individuals in cultural space, a result unaccessible to one-dimensional analyses and in striking contrast with random assumptions. When empirical data are used as inputs in models, we find that ultrametricity has strong and counterintuitive effects, especially in the extreme case of long-range online-like interactions bypassing social ties. On short time-scales, it strongly facilitates a symmetry-breaking phase transition triggering coordinated social behavior. On long time-scales, it severely suppresses cultural convergence by restricting it within disjoint groups. We therefore find that, remarkably, the empirical distribution of individuals in cultural space appears to optimize the coexistence of short-term collective behavior and long-term cultural diversity, which can be realized simultaneously for the same moderate level of mutual influence

Use of mixed study techniques in the evaluation of coastline dynamics - the “Porto Cesareo” MPA case of study

In recent decades, the much-discussed climate changes with the consequent variations in sea and weather conditions and the rise of the mean sea level are causing an indisputable set of negative actions on the entire coastal system mainly due to the increase of the erosive phenomenon along the shorelines. These critical scenarios have a major impact even on a local scale, and because of that, we decided to study a well knows tract of rocky/sandy mixed coast, in a highly anthropized area, even if located inside the “Porto Cesareo” Marine Protected Area (MPA) (Ionian Sea, Gulf of Taranto, Puglia Region, Italy). The high naturalistic and archaeological value of this area calls for a greater institutional effort in the study of erosional phenomena. Several historical documents from other studies point out that this coastal area is an ideal place for this kind of research. The effects of coastal erosion and anthropic pressures along this tract of coast require adequate efforts for a consistent and rapid evaluation of the coastal dynamics. The methodologies proposed in this work are based on mixed techniques from different fields of study, integrating recent aero photogrammetry surveys with drones, aerial images acquired by the Italian Military Geographic Institute (IGM), elaboration of paleoshorelines related by underwater archaeological markers and their dating, and finally on the elaboration of satellite products useful for the study of vast areas. The monitoring of coastal areas and the evaluation of shoreline dynamics are core topics in the implementation of managing actions of decision makers on a local, regional, national, and international scale, above all in places like the chosen one, inside an MPA. Remote sensing through the use of RPAS (Remotely Piloted Aircraft Systems or Drones) has proved to be very useful for identifying phenomena that act on a small spatial scale and in supporting and implementing protective measures according to the adaptive management approach, through multi-year surveys on habitats of conservation interest [18]. For the implementation of fine-scale monitoring actions, we have chosen products from the Sentinel satellite of the Copernicus constellation (European Space Agency - ESA). In this context, the use of satellite products provides a recurrent view of the ground, useful in the short and long-term monitoring of changes in wide coastal areas, and in particular, offers a coastline positioning evaluation in near real-time. Local monitoring actions performed in recent years have already shown an erosive trend in the past decades, and even, negative forecasts for the next decade, so further surveys with mixed methodologies could be crucial in the evaluation of the evolution of this particular coastal area by local authorities

Application of firefly luciferase assay for adenosine triphosphate (ATP) to antimicrobial drug sensitivity testing

The development of a rapid method for determining microbial susceptibilities to antibiotics using the firefly luciferase assay for adenosine triphosphate (ATP) is documented. The reduction of bacterial ATP by an antimicrobial agent was determined to be a valid measure of drug effect in most cases. The effect of 12 antibiotics on 8 different bacterial species gave a 94 percent correlation with the standard Kirby-Buer-Agar disc diffusion method. A 93 percent correlation was obtained when the ATP assay method was applied directly to 50 urine specimens from patients with urinary tract infections. Urine samples were centrifuged first to that bacterial pellets could be suspended in broth. No primary isolation or subculturing was required. Mixed cultures in which one species was predominant gave accurate results for the most abundant organism. Since the method is based on an increase in bacterial ATP with time, the presence of leukocytes did not interfere with the interpretation of results. Both the incubation procedure and the ATP assays are compatible with automation

Use of a novel sharp-tip, J-shaped guidewire to facilitate transseptal catheterization

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