Group Testing Algorithms: Bounds and Simulations

We consider the problem of nonadaptive noiseless group testing of N items of which K are defective. We describe four detection algorithms, the COMP algorithm of Chan et al., two new algorithms, DD and SCOMP, which require stronger evidence to declare an item defective, and an essentially optimal but computationally difficult algorithm called SSS. We consider an important class of designs for the group testing problem, namely those in which the test structure is given via a Bernoulli random process. In this class of Bernoulli designs, by considering the asymptotic rate of these algorithms, we show that DD outperforms COMP, that DD is essentially optimal in regimes where K ≥ √N, and that no algorithm can perform as well as the best nonrandom adaptive algorithms when K > N 0.35 . In simulations, we see that DD and SCOMP far outperform COMP, with SCOMP very close to the optimal SSS, especially in cases with larger K

Almost separable matrices

An m×n matrix A with column supports {Si} is k-separable if the disjunctions ⋃i∈KSi are all distinct over all sets K of cardinality k. While a simple counting bound shows that m>klog2n/k rows are required for a separable matrix to exist, in fact it is necessary for m to be about a factor of k more than this. In this paper, we consider a weaker definition of ‘almost k-separability’, which requires that the disjunctions are ‘mostly distinct’. We show using a random construction that these matrices exist with m=O(klogn) rows, which is optimal for k=O(n1−β) . Further, by calculating explicit constants, we show how almost separable matrices give new bounds on the rate of nonadaptive group testing

A kinetic study of gamma-glutamyltransferase (GGT)-mediated S-nitrosoglutathione catabolism.

S-Nitrosoglutathione (GSNO) is a nitric oxide (NO) donor compound which has been postulated to be involved in transport of NO in vivo. It is known that c-glutamyl transpeptidase (GGT) is one of the enzymes involved in the enzyme-mediated decomposition of GSNO, but no kinetics studies of the reaction GSNO-GGT are reported in literature. In this study we directly investigated the kinetics of GGT with respect to GSNO as a substrate and glycyl- glycine (GG) as acceptor co-substrate by spectrophotometry at 334 nm. GGT hydrolyses the c-glutamyl moiety of GSNO to give S-nitroso-cysteinylglycine (CGNO) and c-glutamyl-GG. However, as both the substrate GSNO and the first product CGNO absorb at 334 nm, we optimized an ancillary reaction coupled to the enzymatic reaction, based on the copper-mediated decomposition of CGNO yielding oxidized cysteinyl-glycine and NO. The ancillary reaction allowed us to study directly the GSNO/GGT kinetics by following the decrease of the characteristic absorbance of nitrosothiols at 334 nm. A Km of GGT for GSNO of 0.398 ± 31 mM was thus found, comparable with Km values reported for other c-glutamyl substrates of GGT

Sistemas agrícolas y silvopastoriles en el Chaco Semiárido. Impactos sobre la productividad primaria

La productividad primaria neta (PPN) se define como la tasa a la cual se acumula biomasa por unidad de área y de tiempo, y se la considera una variable integradora del funcionamiento de los ecosistemas. El desmonte y los cambios en el uso del suelo que afectan gran parte de la región del Chaco Semiárido pueden impactar sobre las ganancias totales de C y su estacionalidad. Trabajos previos en la región utilizan índices espectrales de vegetación como subrogado de la PPN. Sin embargo, arriban a resultados dispares y sólo se circunscriben a lo que sucede con la parte aérea (PPNA), sin considerar los cambios que ocurren en la porción subterránea (PPNS), que suele variar entre tipos fisonómicos de vegetación. Sobre la base del modelo de eficiencia en el uso de la radiación, de información espectral derivada de sensores remotos y de relaciones PPNS/PPN de la bibliografía, el objetivo de este trabajo fue cuantificar el efecto de la transformación en el uso y la cobertura del suelo sobre la PPN, y su variación estacional. En particular, se evaluó el cambio de la PPN en sistemas agrícolas y silvopastoriles con un componente leñoso variable, respecto del bosque original. En general, se observó que los usos del suelo que presentaban una mayor productividad aérea mostraban, al mismo tiempo, los menores niveles de productividad subterránea. El doble cultivo trigo-maíz presentó la mayor PPN total, significativamente superior a la de los sistemas silvopastoriles entre 5 y 25% de cobertura arbórea, y a los cultivos de trigo-soja y soja de primera. Sin embargo, su productividad no varió significativamente de la del bosque, las pasturas megatérmicas y el maíz de primera. Los resultados obtenidos no sólo aportan información sustancial para concluir cuantitativamente en términos de la magnitud del cambio en unidades de materia seca, sino que también permiten establecer un orden o ranking más apropiado de las coberturas y usos del suelo en cuanto a la productividad total

Carbon stocks and potential sequestration of Uruguayan soils: a road map to a comprehensive characterization of temporal and spatial changes to assess carbon footprint

Carbon net emission is a critical aspect of the environmental footprint in agricultural systems. However, the alternatives to describe soil organic carbon (SOC) changes associated with different agricultural management practices/land uses are limited. Here we provide an overview of carbon (C) stocks of non-forested areas of Uruguay to estimate SOC changes for different soil units affected by accumulated effects of crop and livestock production systems in the last decades. For this, we defined levels based on SOC losses relative to the original (reference) SOC stocks: 25% or less, between 25% and 50%, and 50% or more. We characterized the reference SOC stocks using three approaches: (1) an equation to derive the potential SOC capacity based on the clay and fine silt soil content, (2) the DayCent model to estimate the SOC stocks based on climate, soil texture and C inputs from the natural grasslands of the area, (3) an estimate of SOC using a proxy derived from remote sensing data (i.e., the Ecosystem Services Supply Index) that accounts for differences in C inputs. Depending on the used reference SOC, the soil units had different distributions of SOC losses within the zones defined by the thresholds. As expected, the magnitude of SOC changes observed for the different soil units was related to the relative frequency of annual crops, however, the high variability observed along the gradient of land uses suggests a wide space for increasing SOC with agricultural management practices. The assessment of the C stock preserved (CSP) belowground and the potential for increasing C accumulation or sequestration (CAP) are critical components of the C footprint of a given system. Thus, we propose a methodological road map to derive indicators of CSP and CAP at the farm level combining both, biogeochemical simulation models and conceptual models based on remote sensing data. We recognize at least three critical issues that require scientific and political consensus to implement the use of this propose: (1) how to define reference C stocks, (2) how to estimate current C stocks over large areas and in heterogeneous agricultural landscapes, and (3) what is a reasonable/acceptable threshold of C stocks reduction

Fracionamento de cobre em proteínas do plasma, músculo e fígado de tilápia do Nilo

Copper fractionation in plasma, muscle and liver of Nile tilapia was performed after protein separation by 2D-PAGE. SR XRF analysis indicated the presence of copper in three protein spots of plasma, and in two protein spots of muscle and liver, respectively. Copper ions were found to be distributed mostly in proteins that had a molar mass of less than 54 kDa and greater than 13 kDa and a pI in the 5.3-9.3 range. The copper concentration bound to these proteins was determined by GFAAS which showed concentrations in the 1.20-4.82 mg g-1 range

Interdisciplina: una oportunidad para entender los sistemas ambientales.

El presente trabajo tiene como objetivo hacer una breve discusión sobre el tema de la interdisciplinariedad. La información fueron obtenida durante el formación “Análisis de los Cambios En El uso y la Tierra de agua y la Seguridad en la Cuenca de alimentaria del Plata”, patrocinado por el Instituto de Capacitación del IAI en abril de 2011, en Asunción, Paraguay. En el programa se debatieron en el uso de conceptos de cambios de la tierra y, y los impulsores naturales humana de los cambios; la cobertura de la tierra, el de la cubierta (la geomorfología y el clima; perturbaciones inducidas y naturales por el hombre, la demanda de alimentos, fibra, y energía: expansión deforestación y de los ecosistemas agrícolas, la demanda de agua (riego, consumo). La interdisciplinariedad surge como una oportunidad de análisis, teniendo en cuenta la diversidad de temas a considerar en los estudios de los cambios en el uso de la tierra.bitstream/item/61880/1/Doc-136-Interdisciplina-Final.pd

Elementos conceptuales y metodológicos para la evaluación de impactos ambientales acumulativos (eiaac) en bosques subtropicales : el caso del este de salta, argentina

163-178Northern Argentina experienced an unprecedented deforestation rate of xerophitic forests as a consequence of agricultural expansion. In the Province of Salta, 26 percent of the forest were removed between 1977 and 2008. At the end of 2007, just before the No. 26331 Law of Native Forest Protection was voted by the Congress, the highest annual rate of deforestation was registered, reaching a value of 2.1 percent. Regarding this situation, indigenous people of Eastern Salta along with the "criollos" (local small ranchers) appealed to the National Supreme Court of Justice for legal protection. The Court requested the province to elaborate a Cumulative Environmental Effects Assessment (CEEA) regarding the process of logging and deforestation in four departments of Salta Province (San Martín, Rivadavia, Santa Victoria, and Orán). The aim of this work is to present a conceptual framework to conduct a CEEA in eastern Salta and to present the evidences and existing methodologies to characterize the impacts of deforestation. The conceptual framework suggested depends on the quantitative characterization of the changes in the provision level of key ecosystem services as a function of the stress and/or disturbance level (in this case deforestation). Based on the literature and our own data, the effects of deforestation on four key ecosystem services have been assessed: C dynamics, energy balance and greenhouse gases emissions, water dynamics and landscape structure. Deforestation produced emissions of 2000 t of CH 4, 200 t of N 2O, above 20 Gg of C/year, a 1.1 watt/m2 reduction in reflected radiation and 4400 TJ radiative energy emissions caused by deforestation fires, increases in the risk of soil salinization and landscape fragmentation. Considering these aspects of the structure and functioning of the ecosystems provides objective elements to evaluate management alternatives and to elaborate monitoring programmes. To consider such management and monitoring alternatives arises technical challenges but also institutional and political ones

Adherence issues related to sublingual immunotherapy as perceived by allergists

Objectives: Sublingual immunotherapy (SLIT) is a viable alternative to subcutaneous immunotherapy to treat allergic rhinitis and asthma, and is widely used in clinical practice in many European countries. The clinical efficacy of SLIT has been established in a number of clinical trials and meta-analyses. However, because SLIT is self-administered by patients without medical supervision, the degree of patient adherence with treatment is still a concern. The objective of this study was to evaluate the perception by allergists of issues related to SLIT adherence. Methods: We performed a questionnaire-based survey of 296 Italian allergists, based on the adherence issues known from previous studies. The perception of importance of each item was assessed by a VAS scale ranging from 0 to 10. Results: Patient perception of clinical efficacy was considered the most important factor (ranked 1 by 54% of allergists), followed by the possibility of reimbursement (ranked 1 by 34%), and by the absence of side effects (ranked 1 by 21%). Patient education, regular follow-up, and ease of use of SLIT were ranked first by less than 20% of allergists. Conclusion: These findings indicate that clinical efficacy, cost, and side effects are perceived as the major issues influencing patient adherence to SLIT, and that further improvement of adherence is likely to be achieved by improving the patient information provided by prescribers. © 2010 Scurati et al, publisher and licensee Dove Medical Press Ltd