ABSTRACT
The use of acoustic Doppler current profilers (ADCP) for discharge measurements and three‐dimensional flow mapping has increased rapidly in recent years and has been primarily driven by ...advances in acoustic technology and signal processing. Recent research has developed a variety of methods for processing data obtained from a range of ADCP deployments and this paper builds on this progress by describing new software for processing and visualizing ADCP data collected along transects in rivers or other bodies of water. The new utility, the Velocity Mapping Toolbox (VMT), allows rapid processing (vector rotation, projection, averaging and smoothing), visualization (planform and cross‐section vector and contouring), and analysis of a range of ADCP‐derived datasets. The paper documents the data processing routines in the toolbox and presents a set of diverse examples that demonstrate its capabilities. The toolbox is applicable to the analysis of ADCP data collected in a wide range of aquatic environments and is made available as open‐source code along with this publication. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.
Purpose: This study was motivated by the need for better positron emission tomography (PET)-compatible tools to image bacterial infection. Our previous efforts have targeted bacteria-specific ...metabolism via assimilation of carbon-11 labeled d-amino acids into the bacterial cell wall. Since the chemical determinants of this incorporation are not fully understood, we sought a high-throughput method to label d-amino acid derived structures with fluorine-18. Our strategy employed a chemical biology approach, whereby an azide (-N3) bearing d-amino acid is incorporated into peptidoglycan muropeptides, with subsequent “click” cycloaddition with an 18F-labeled strained cyclooctyne partner. Procedures: A water-soluble, 18F-labeled and dibenzocyclooctyne (DBCO)-derived radiotracer (18FFB-sulfo-DBCO) was synthesized. This tracer was incubated with pathogenic bacteria treated with azide-bearing d-amino acids, and incorporated 18F was determined via gamma counting. In vitro uptake in bacteria previously treated with azide-modified d-amino acids was compared to that in cultures treated with amino acid controls. The biodistribution of 18FFB-sulfo-DBCO was studied in a cohort of healthy mice with implications for future in vivo imaging. Results: The new strain-promoted azide–alkyne cycloaddition (SPAAC) radiotracer 18FFB-sulfo-DBCO was synthesized with high radiochemical yield and purity via N-succinimidyl 4-18Ffluorobenzoate (18FSFB). Accumulation of 18FFB-sulfo-DBCO was significantly higher in several bacteria treated with azide-modified d-amino acids than in controls; for example, we observed 7 times greater 18FFB-sulfo-DBCO ligation in Staphylococcus aureus cultures incubated with 3-azido-d-alanine versus those incubated with d-alanine. Conclusions: The SPAAC radiotracer 18FFB-sulfo-DBCO was validated in vitro via metabolic labeling of azide-bearing peptidoglycan muropeptides. d-Amino acid-derived PET radiotracers may be more efficiently screened via 18FFB-sulfo-DBCO modification.
Runoff transports nutrients and impoverishes agricultural soils, causing off-site environment contamination. The objective of this study was to quantify P, K and organic carbon concentrations in ...runoff under different soil tillage systems. The experiment was carried out in the field, under simulated rainfall, during soybean growth, from April 2003 to May 2004, in the Santa Catarina highlands, Southern Brazil, on a typical Hapludox. The evaluated soil tillage treatments (which were replicated) were: (i) continuous bare soil (BS), (ii) conventional tillage on a desiccated residue (CT), (iii) no till on a burned residue, in a never-tilled soil (BNT), (iv) no till on a desiccated residue, in a never-tilled soil (DNTnt) and (v) no till on a desiccated residue, in soil tilled 4 years before (DNTt). Fodder radish (
Raphanus sativus) residues were managed as indicated prior to planting soybean crop. As a result, no-till treatments have higher P, K and organic carbon concentrations in the superficial 0–0.025
m soil layer and in runoff sediments than CT. The highest enrichment ratios were of 0.90, 1.34 and 1.17 for P, K and organic carbon, and occurred in burned no till, bare soil and conventional treatments, respectively. P and K concentrations in runoff water reached in the first rainfall test 1.0 and 15.8
mg
L
−1 in the no-till treatments, and were higher than in the CT treatment, where these contents were only of 0.09 and 1.9
mg
L
−1, respectively. Crop residue burning increased P and K and reduced organic carbon levels in the topsoil layer compared to other non-burned treatments. In the runoff water, burning increased P and K concentrations, while in sediments, it presented higher P and organic carbon contents and reduced K levels, in relation to non-burned plots. Positive linear correlations were obtained between P and K in runoff water and P, K and organic carbon in sediments, and their respective levels in the 0–0.025
m soil layer. P and K concentrations in runoff water decreased exponentially in the no-till treatments, and linearly in CT and BS with the number of rains applied. P contents in sediments exponentially decreased, while K potentially increased with the size of the particles in the sediments transported in runoff. There was no relationship between organic carbon content in runoff sediments loss and sediment size.
Abstract
Background
Vertebral discitis-osteomyelitis (VDO) is a devastating infection of the spine that is challenging to distinguish from noninfectious mimics using computed tomography and magnetic ...resonance imaging. We and others have developed novel metabolism-targeted positron emission tomography (PET) radiotracers for detecting living Staphylococcus aureus and other bacteria in vivo, but their head-to-head performance in a well-validated VDO animal model has not been reported.
Methods
We compared the performance of several PET radiotracers in a rat model of VDO. 11CPABA and 18FFDS were assessed for their ability to distinguish S aureus, the most common non-tuberculous pathogen VDO, from Escherichia coli.
Results
In the rat S aureus VDO model, 11CPABA could detect as few as 103 bacteria and exhibited the highest signal-to-background ratio, with a 20-fold increased signal in VDO compared to uninfected tissues. In a proof-of-concept experiment, detection of bacterial infection and discrimination between S aureus and E coli was possible using a combination of 11CPABA and 18FFDS.
Conclusions
Our work reveals that several bacteria-targeted PET radiotracers had sufficient signal to background in a rat model of S aureus VDO to be potentially clinically useful. 11CPABA was the most promising tracer investigated and warrants further investigation in human VDO.
Soil tillage may increase vulnerability to water erosion, whereas no tillage and other conservation cultivation techniques are viewed as strategies to control soil erosion. The objective of this ...research was to quantify runoff and soil losses by water erosion under different soil tillage systems at the Santa Catarina Highlands, southern Brazil. A field study was carried out using a rotating-boom rainfall simulator with 64
mm
h
−1 rainfall intensity on a Typic Hapludox, between April 2003 and May 2004. Five rainfall tests were applied along successive cropstages. Surface cover was none (fallow) or soybean (
Glycine max, L.). Five treatments were investigated, replicated twice. These treatments were conventional tillage on bare soil (BS) as a control treatment and the following treatments under soybean: conventional tillage (CT), no tillage over burnt crop residues on never before cultivated land (NT-B), no tillage over desiccated crop residues, also on never before cultivated land (NT-D) and traditional no tillage over desiccated crop residues on a soil tilled 4 years before this experiment (NT-PT). Water losses by surface runoff seemed to be more influenced by vegetative crop stadium than by tillage system and consequently a wide range of variation in surface runoff was found, following successive cropstages. The most efficient tillage system in reducing surface runoff and soil losses was no tillage, particularly the NT-PT treatment. Sediment losses were more influenced by tillage system than water losses. In the NT-B, NT-D and NT-PT treatments the rate of sediment losses along the crop vegetative cycle showed a tendency to increase from the first to the second cropstages and later to decrease from the third cropstage onwards. In the conventionally tilled treatment (CT) soil losses were greater than in any of the no tillage treatments (NT-D, NT-B and NT-PT) during the initial growth periods, but at the end of the vegetative period differences in sediment rates between tilled and non-tilled treatments tended to be smaller. In the BS control treatment, soil losses progressively increased following the vegetative growth season of soybean.
The European Union 1997 Directive, stipulating that veal calves should be fed a minimum of 50 to 250g of fibrous feed from 8 to 20wk of age, is vague. A fibrous feed ration maximum of 250g has been ...implicated in welfare issues, namely the occurrence of abnormal oral behaviors and poor gastrointestinal health. Past research suggests that this amount is insufficient to prevent the development of abnormal oral behaviors and enabling good rumen development. Different sources and particle sizes of roughage could lead to very different welfare outcomes. In a 3×2 × 2 factorial design, 240 group-housed calves (10±1d; 46.1±0.1kg) were fed different roughage sources (straw, maize silage, or maize cob silage; the latter 2 were dried and provided no extra moisture compared with straw) in 2 amounts (250 or 500g of dry matter per day), and 2 particle sizes (chopped or ground). Roughage was supplemented to milk replacer (MR) from 2wk after arrival. In addition, 60 calves were fed 1 of 3 additional control treatments: MR only (n=20), MR plus an iron supplement (n=20), or MR plus ad libitum hay (n=20). Oral behaviors were recorded using instantaneous scan sampling at 2-min intervals for 2h in 3 periods per day, at 12 and 22wk of age. Calves were slaughtered at 24wk of age and rumen and abomasal health parameters were recorded. Limited provision of straw resulted in behavior comparable with that from unlimited provision of hay, with reduced tongue playing and oral manipulation of the environment, as well as increased chewing compared with diets with no roughage supplement. Straw prevented ruminal hairballs, but impaired rumen development and increased abomasal damage. A higher ration of roughage increased chewing (12wk), decreased oral manipulation of the trough (12 and 22wk) and the pen (22wk), and increased rumen weight. However, more roughage led to increased abomasal damage for certain parameters. Longer feed particles had no obvious benefits for behavior, but decreased hairball prevalence. Overall, unlimited hay had the highest benefit for both behavior and gastrointestinal health. Adding iron to the MR did not alter behavior or gastrointestinal health compared with MR without iron supplement. This study demonstrated that different roughage sources, amounts, and particle sizes have different effects on veal calf behavior and gastrointestinal health, and hence on veal calf welfare.
The study aimed at assessing the prevalence of poor rumen development, presence of rumen plaques, rumen papillae hyperkeratinization, and abomasal lesions in veal calves and to investigate risk ...factors for their occurrence at the farm level. Within a wide cross-sectional study, a sample of 170 veal farms representative of the European veal meat production systems was considered in the 3 major producing countries (99 in the Netherlands, 47 in France, and 24 in Italy). An average of 59±10 (SD) rumens and abomasa belonging to calves from a single batch per farm were inspected at the abattoir by trained observers to assess the incidence of these gastrointestinal disorders. Potential risk factors for their occurrence related to farm management, housing, and to the feeding plan were obtained by a questionnaire submitted to the stockperson. Prevalence of poor rumen development (almost no papillae present), rumen plaques, and hyperkeratinization were 60.4, 31.4, and 6.1% of rumens, respectively, whereas abomasal lesions in the pyloric area were recorded in 74.1% of abomasa. Independent variables related to the feeding system confirmed to be the main risk factors for the occurrence of gastrointestinal disorders in veal calves. However, additional risk sources for each given problem were identified among housing and management variables. The provision of a low amount of solid feed (≤50kg of dry matter/head per cycle) was a relevant risk for rumen underdevelopment. Rumen wall alterations (plaques and hyperkeratinization) and abomasal lesions were instead associated with the administration of large quantities of solids (151–300kg of dry matter/head per cycle) in calves receiving milk replacer during the entire fattening cycle. Among the types of solid feed, cereal grain acted as a preventive measure for low rumen development, whereas it was a risk factor for the occurrence of rumen plaques, papillae hyperkeratinization, and abomasal lesions. Some housing and management options adopted to improve veal calf welfare (i.e., higher space allowance and use of heating) were associated with lower risk for gastrointestinal disorders.
A rectal culture-guided antimicrobial prophylaxis strategy may prevent infections after transrectal ultrasound-guided prostate biopsy (TRUSP). The use of selective culture media could assist the ...choice of appropriate antibiotic prophylaxis. The objective of our study was to evaluate the performance of four selective media used for guidance of oral antibiotic prophylaxis in TRUSP. In this prospective validation study, we used MacConkey media with vancomycin plus one of the following antibiotics: ciprofloxacin (McC3+CIP/V), trimethoprim (McC3+TMP/V), fosfomycin (McC3+FOF/V), and amdinocillin-amoxicillin-clavulanic acid (McC3+MEC/V). First, clinical strains of Gram-negative bacilli (GNB) (
= 33) were evaluated for growth on the selective media. Thereafter, rectal swabs (
= 97) were randomly collected from residual material of fresh stool samples and plated on a growth control and the four selective media. Levels of recovery of GNB on the growth control and selective media were compared, and the MICs of the antibiotics used in this study were determined. The sensitivity and specificity of the four selective media amounted, respectively, to 90.0% (55.5 to 99.8%) and 98.7% (93.1 to 100.0%) for McC3+CIP/V, 95.7% (85.2 to 99.5%) and 100.0% (91.6 to 100.0%) for McC3+TMP/V, 95.5% (84.5 to 99.4%) and 97.8% (88.2 to 99.9%) for McC3+FOF/V, and 100.0% (76.8 to 100.0%) and 97.6% (87.4 to 99.9%) for McC3+MEC/V. In conclusion, the four selective media were sufficiently sensitive and specific for the identification of rectal GNB resistant to ciprofloxacin, trimethoprim, fosfomycin, or amdinocillin-amoxicillin-clavulanic acid. These media can have added value in streamlining the optimal culture based antibiotic prophylaxis in TRUSP in a non-labor-intensive manner.
Imaging is increasingly used to detect and monitor bacterial infection. Both anatomic (X-rays, computed tomography, ultrasound, and MRI) and nuclear medicine (111In-WBC SPECT, 18FFDG PET) techniques ...are used in clinical practice but lack specificity for the causative microorganisms themselves. To meet this challenge, many groups have developed imaging methods that target pathogen-specific metabolism, including PET tracers integrated into the bacterial cell wall. We have previously reported the d-amino acid derived PET radiotracers d-methyl-11C-methionine, d-3-11C-alanine, and d-3-11C-alanine-d-alanine, which showed robust bacterial accumulation in vitro and in vivo. Given the clinical importance of radionuclide half-life, in the current study, we developed 18F3,3,3-trifluoro-d-alanine (d-18F-CF3-ala), a fluorine-18 labeled tracer. We tested the hypothesis that d-18F-CF3-ala would be incorporated into bacterial peptidoglycan given its structural similarity to d-alanine itself. NMR analysis showed that the fluorine-19 parent amino acid d-19F-CF3-ala was stable in human and mouse serum. d-19F-CF3-ala was also a poor substrate for d-amino acid oxidase, the enzyme largely responsible for mammalian d-amino acid metabolism and a likely contributor to background signals using d-amino acid derived PET tracers. In addition, d-19F-CF3-ala showed robust incorporation into Escherichia coli peptidoglycan, as detected by HPLC/mass spectrometry. Based on these promising results, we developed a radiosynthesis of d-18F-CF3-ala via displacement of a bromo-precursor with 18Ffluoride followed by chiral stationary phase HPLC. Unexpectedly, the accumulation of d-18F-CF3-ala by bacteria in vitro was highest for Gram-negative pathogens in particular E. coli. In a murine model of acute bacterial infection, d-18F-CF3-ala could distinguish live from heat-killed E. coli, with low background signals. These results indicate the viability of 18F-modified d-amino acids for infection imaging and indicate that improved specificity for bacterial metabolism can improve tracer performance.
Perforations are known to occur after colonoscopy. In a consecutive study the localization of the perforation was determined, and the etiology of the perforation was classified as: therapeutic, ...barotraumatic or mechanical. A colonic perforation occurred in 26 of 19,135 patients (0.14%). In 13 cases (50.0%) the cause of perforation was mechanical, in nine (34.6%) the cause was a barotrauma (cecal blow-out), and in three cases (11.5%) it was due to a therapeutic procedure (coagulation or polypectomy). In one case (3.8%) data were not available. Cecal blow-out occurred significantly more often as a result of barotrauma, whereas perforation of the sigmoid occurred more often as a result of direct mechanical trauma. The risk of perforation after colonoscopy is rather low. Barotrauma due to insufflated air occurs more often than therapeutic perforation due to polypectomy or coagulation. Patients with a higher risk of perforation are those with diverticula in the sigmoid.
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