Implications of using 2 m versus 30 m spatial resolution data for suburban residential land change modeling

This study assesses the advantages and disadvantages of using 2 m spatial resolution data versus 30 m resolution data for a simulation model of land-use and land-cover change (LUCC). The model projects LUCC from 2005 to 2055 in the town of Lynnfield, Massachusetts, USA. This article describes four scenario storylines and then projects land-use and land-cover under each of the four scenarios with 2 m data and again with 30 m data. The disagreement between the 2 m output and its corresponding 30 m output ranges between 5.7% and 11.0% of the town. The disagreement due to allocation over small distances is greater than the disagreement due to the quantity of new residential growth. The projected quantities of new residential land-use in 2055 differ between the two resolutions by 1% of the town, whereas the visual differences in the spatial allocations are distinct and substantial. The results for this case study show that 30 m resolution data provides several practical and theoretical advantages over 2 m resolution data, due mainly to the fact that the 30 m resolution data match more closely the size of the patches of change

Magnetization of small lead particles

The magnetization of an ensemble of isolated lead grains of sizes ranging from below 6 nm to 1000 nm is measured. A sharp disappearance of Meissner effect with lowering of the grain size is observed for the smaller grains. This is a direct observation by magnetization measurement of the occurrence of a critical particle size for superconductivity, which is consistent with Anderson's criterion.Comment: 7 pages, 5 figures, Submitted to PR

Secondary metabolites of the sponge-derived fungus Acremonium persicinum

This study reports the isolation and characterization of six new acremine metabolites, 5-chloroacremine A (4), 5-chloroacremine H (5), and acremines 0 (6), P (7), Q(8), and R (9), together with the known acremines A (1), F (2), and N (3) from the fungus Acremonium persicinum cultured from the marine sponge Anomoianthella rubra. The relative configuration of acremine F (2) was determined by analyses of proton coupling constant values and NOESY data, and the absolute configuration confirmed as (IS, 4S, 6R) by X-ray crystallographic analysis of the borate ester derivative 15. Acremines O, P, and R were each shown to be of 8R configuration by H-1 NMR analyses of MPA esters. The relative configurations suggested for acremines P and Q were each deduced by molecular modeling together with NOESY and coupling constant data. The (3)J(H-C) values in acremine P were measured using the pulse sequence EXSIDE, and the observed (3)J(H8-C4) of 5.4 Hz and small (3)J(H-C) values

Impact on diarrhoeal illness of a community educational intervention to improve drinking water quality in rural communities in Puerto Rico

<p>Abstract</p> <p>Background</p> <p>Waterborne disease is a major risk for small water supplies in rural settings. This study was done to assess the impact of an educational intervention designed to improve water quality and estimate the contribution of water to the incidence of diarrhoeal disease in poor rural communities in Puerto Rico a two-part study was undertaken.</p> <p>Methods</p> <p>An educational intervention was delivered to communities relying on community water supplies. This intervention consisted of student operators and administrators supervising and assisting community members who voluntarily "operate" these systems. These voluntary operators had no previous training and were principally concerned with seeing that some water was delivered. The quality of that water was not something they either understood or addressed. The impact of this intervention was measured through water sampling for standard bacteriological indicators and a frank pathogen. In addition, face-to-face epidemiological studies designed to determine the base-line occurrence of diarrhoeal disease in the communities were conducted. Some 15 months after the intervention a further epidemiological study was conducted in both the intervention communities and in control communities that had not received any intervention.</p> <p>Results</p> <p>Diarrhoeal illness rates over a four week period prior to the intervention were 3.5%. <it>Salmonella </it>was isolated from all of 5 distributed samples prior to intervention and from only 2 of 12 samples after the intervention. In the 15 months follow-up study, illness rates were lower in the intervention compared to control communities (2.5% <it>vs </it>3.6%%) (RR = 0.70, 95%CI 0.43, 1.15), though this was not statistically significant. However, in the final Poisson regression model living in an intervention system (RR = 0.318; 95%CI 0.137 - 0.739) and owning a dog (RR = 0.597, 95%CI 0.145 - 0.962) was negatively associated with illness. Whilst size of system (RR = 1.006, 95%CI 1.001 - 1.010) and reporting problems with sewage system (RR = 2.973, 95%CI 1.539 - 5.744) were positively associated with illness.</p> <p>Conclusions</p> <p>Educational interventions directed both at identified individuals and the community in general in small communities with poor water quality is a way of giving communities the skills and knowledge to manage their own drinking water quality. This may also have important and sustainable health benefits, though further research preferably using a randomised control trial design is needed.</p

A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat

BACKGROUND: The Affymetrix GeneChip technology uses multiple probes per gene to measure its expression level. Individual probe signals can vary widely, which hampers proper interpretation. This variation can be caused by probes that do not properly match their target gene or that match multiple genes. To determine the accuracy of Affymetrix arrays, we developed an extensive verification protocol, for mouse arrays incorporating the NCBI RefSeq, NCBI UniGene Unique, NIA Mouse Gene Index, and UCSC mouse genome databases. RESULTS: Applying this protocol to Affymetrix Mouse Genome arrays (the earlier U74Av2 and the newer 430 2.0 array), the number of sequence-verified probes with perfect matches was no less than 85% and 95%, respectively; and for 74% and 85% of the probe sets all probes were sequence verified. The latter percentages increased to 80% and 94% after discarding one or two unverifiable probes per probe set, and even further to 84% and 97% when, in addition, allowing for one or two mismatches between probe and target gene. Similar results were obtained for other mouse arrays, as well as for human and rat arrays. Based on these data, refined chip definition files for all arrays are provided online. Researchers can choose the version appropriate for their study to (re)analyze expression data. CONCLUSION: The accuracy of Affymetrix probe sequences is higher than previously reported, particularly on newer arrays. Yet, refined probe set definitions have clear effects on the detection of differentially expressed genes. We demonstrate that the interpretation of the results of Affymetrix arrays is improved when the new chip definition files are used

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

Transposable elements (TEs) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo “clouds”). We show here that P-clouds predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%–69% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both P-clouds and a commonly used conventional approach, RepeatMasker (RM), to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to P-clouds, which has good sensitivity down to small fragment sizes (∼25 bp). Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed “element-specific” P-clouds (ESPs) to identify novel Alu and MIR SINE elements, and using it we identified ∼100 Mb of previously unannotated human elements. ESP estimates of new MIR sequences are in good agreement with RM-based predictions of the amount that RM missed. These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed

On-line analysis and in situ pH monitoring of mixed acid fermentation by Escherichia coli using combined FTIR and Raman techniques

We introduce an experimental setup allowing continuous monitoring of bacterial fermentation processes by simultaneous optical density (OD) measurements, long-path FTIR headspace monitoring of CO2, acetaldehyde and ethanol, and liquid Raman spectroscopy of acetate, formate, and phosphate anions, without sampling. We discuss which spectral features are best suited for detection, and how to obtain partial pressures and concentrations by integrations and least squares fitting of spectral features. Noise equivalent detection limits are about 2.6 mM for acetate and 3.6 mM for formate at 5 min integration time, improving to 0.75 mM for acetate and 1.0 mM for formate at 1 h integration. The analytical range extends to at least 1 M with a standard deviation of percentage error of about 8%. The measurement of the anions of the phosphate buffer allows the spectroscopic, in situ determination of the pH of the bacterial suspension via a modified Henderson-Hasselbalch equation in the 6–8 pH range with an accuracy better than 0.1. The 4 m White cell FTIR measurements provide noise equivalent detection limits of 0.21 μbar for acetaldehyde and 0.26 μbar for ethanol in the gas phase, corresponding to 3.2 μM acetaldehyde and 22 μM ethanol in solution, using Henry’s law. The analytical dynamic range exceeds 1 mbar ethanol corresponding to 85 mM in solution. As an application example, the mixed acid fermentation of Escherichia coli is studied. The production of CO2, ethanol, acetaldehyde, acids such as formate and acetate, and the changes in pH are discussed in the context of the mixed acid fermentation pathways. Formate decomposition into CO2 and H2 is found to be governed by a zeroth-order kinetic rate law, showing that adding exogenous formate to a bioreactor with E. coli is expected to have no beneficial effect on the rate of formate decomposition and biohydrogen production