Simrank: Rapid and sensitive general-purpose k-mer search tool

Background  

Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project . Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available.     

Tunneling into a single magnetic atom: spectroscopic evidence of the kondo resonance

The Kondo effect arises from the quantum mechanical interplay between the electrons of a host metal and a magnetic impurity and is predicted to result in local charge and spin variations around the magnetic impurity. A cryogenic scanning tunneling microscope was used to spatially resolve the electronic properties of individual magnetic atoms displaying the Kondo effect. Spectroscopic measurements performed on individual cobalt atoms on the surface of gold show an energetically narrow feature that is identified as the Kondo resonance-the predicted response of a Kondo impurity. Unexpected structure in the Kondo resonance is shown to arise from quantum mechanical interference between the d orbital and conduction electron channels for an electron tunneling into a magnetic atom in a metallic host.     

Partial Hepatectomy with Temporary Hepatic Vascular Occlusion in Dogs with Hepatic Arteriovenous Fistulas

A technique for temporary hepatic vascular occlusion during partial hepatectomy for hepatic arteriovenous (AV) fistulas in the dog is presented in seven dogs, and three additional cases of hepatic AV fistulas are reviewed. Hematologic, serum biochemical, radiologic, and nuclear scintigraphic parameters before and after surgery are discussed; abnormalities included anemia, hypoproteinemia, leukocytosis, increased liver function tests, retrograde filling of the portal vein during celiac angiography, and increased arteriovenous ratios during nuclear scintigraphy. Hemodynamic and pathologic findings are presented, and portal hypertension and secondary multiple portosystemic shunts are described. Clinical improvement was observed in four dogs with follow-up periods ranging from 5 months to 3 years.     

A review of black heart of ash (Fraxinus excelsior L.)

Black heart is a non-fungal stain of ash (Fraxinus excelsiorL.) which results in a price penalty compared with white wood.The formation of black heart varies within individual trees,between trees and on different sites; the evidence availablesuggests that it can be present in up to 45 per cent of treesat age 60. Once formed the proportion of cross-sectional areaaffected increases with age. Previous work has suggested thatblack heart has no effect on timber properties or strength butits occurrence has been linked with high soil moisture. Howeverthese studies were conducted in the 1950s and need to be confirmedusing more rigorous research methods. Scope exists for innovativemarketing of black heartwood to emphasize that it is a naturalfeature and can be visually pleasing; this may lead to betterreturns for the grower.     

集成定量方法用于同时监控密集型农业区域土壤侵蚀和非点源污染状况的研究

In China, some areas with intensive agricultural use are facing serious environmental problems caused by non-point source pollution（NPSP） as a consequence of soil erosion（SE）. Until now, simultaneous monitoring of NPSP and SE is difficult due to the intertwined effects of crop type, topography and management in these areas. In this study, we developed a new integrated method to simultaneously monitor SE and NPSP in an intensive agricultural area（about 6 000 km2） of Nanjing in eastern China, based on meteorological data,a geographic information system database and soil and water samples, and identified the main factors contributing to NPSP and SE by calculating the NPSP and SE loads in different sub-areas. The levels of soil total nitrogen（TN）, total phosphorus（TP）, available nitrogen（AN） and available phosphorus（AP） could be used to assess and predict the extent of NPSP and SE status in the study area.The most SE and NPSP loads occurred between April to August. The most seriously affected area in terms of SE and NPSP was the Jiangning District, implying that the effective management of SE and NPSP in this area should be considered as a priority. The sub-regions with higher vegetation coverage contributed to less SE and NPSP, confirming the conclusions of previous studies, namely that vegetation is an effective factor controlling SE and NPSP. Our quantitative method has both high precision and reliability for the simultaneous monitoring of SE and NPSP occurring in intensive agricultural areas.     

Size fractions of organic matter pools influence their stability: Application of the Rock-Eval® analysis to beech forest soils

Soil organic matter (SOM) is a complex heterogeneous mixture formed through decomposition and organo-mineral interactions, and characterization of its composition and biogeochemical stability is challenging. From this perspective, Rock-Eval^® is a rapid and efficient thermal analytical method that combines the quantitative and qualitative information of SOM, including several parameters related to thermal stability. This approach has already been used to monitor changes in organic matter (OM) properties at the landscape, cropland, and soil profile scales. This study was aimed to assess the stability of SOM pools by characterizing the grain size fractions from forest litters and topsoils using Rock-Eval^® thermal analysis. Litter (organic) and topsoil samples were collected from a beech forest in Normandy (France), whose management in the last 200 years has been documented. Fractionation by wet sieving was used to separate large debris (> 2 000 μm) and coarse (200-2 000 μm) and fine particulate OM (POM) (50-200 μm) in the organic samples as well as coarse (200-2 000 μm), medium (50-200 μm), and fine (< 50 μm) fractions of the topsoil samples. Rock-Eval^® was able to provide thermal parameters sensitive enough to study fine-scale soil processes. In the organic layers, quantitative and qualitative changes were explained by the progressive decomposition of labile organic compounds from plant debris to the finest organic particles. Meanwhile, the grain size fractions of topsoils presented different characteristics. The coarse organo-mineral fractions showed higher C contents, albeit with a different composition, higher thermal stability, and greater decomposition degree than the plant debris forming the organic layer. These results are consistent with those of previous studies that microbial activity is more effective in this fraction. The finest fractions of topsoils showed low C contents, the highest thermal stability, and low decomposition degree, which can be explained by the stronger interactions with the mineral matrix. Therefore, it is suggested that the dynamics of OM in the different size fractions be interpreted in the light of a plant-microbe-soil continuum. Finally, three distinct thermostable C pools were highlighted through the grain size heterogeneity of SOM:free coarse OM (large debris and coarse and fine particles), weakly protected OM in (bio)aggregates (coarse fraction of topsoil), and stabilized OM in the fine fractions of topsoil, which resulted from the interactions within organo-mineral complexes. Therefore, Rock-Eval^® thermal parameters can be used to empirically illustrate the conceptual models emphasizing the roles of drivers played by the gradual decomposition and protection of the most thermally labile organic constituents.     

High Embryonic Recovery Rates with In vivo and Ex vivo Techniques in the Bitch

The embryonic collection techniques in dogs present a vast methodological variation and low recovery rates. The objectives were to compare and describe two techniques as to the recovery of canine embryos, on the 12th day after the first mating or artificial insemination. Embryos were recovered through uterine horn flushing in vivo, before performing the ovariohysterectomy (OHE) (Group 1; n = 9) or ex vivo, immediately after the OHE (Group 2; n = 9). In total, 43 and 47 embryonic structures were recovered in Groups 1 and 2, respectively. There was no significant difference (p > 0.05) between groups on recovery rates (72.8% and 81.0%, respectively). We inferred that both in vivo and ex vivo techniques allow a high rate of embryonic recovery; in the collection technique prior to the OHE, it is essential to carefully handle the reproductive system during the trans‐surgical period and that the 12th day (D12) after the first mating/artificial insemination is an efficient option for the high recovery rate of morulae and blastocysts.     

Population pharmacokinetic modelling and simulation of single and multiple dose administration of meloxicam in cats

Lehr, T., Narbe, R., Jöns, O., Kloft, C., Staab, A. Population pharmacokinetic modelling and simulation of single and multiple dose administration of meloxicam in cats. J. vet. Pharmacol. Therap. 33 , 277–286. The objectives of these investigations were: first, to describe the pharmacokinetic properties of meloxicam in cats following single and multiple oral administration and secondly, to simulate different oral dosage regimes for meloxicam in cats after multiple dose administration to illustrate and evaluate those dosage regimes for the alleviation of inflammation and pain in cats. Six healthy domestic short hair cats were treated orally with various dosage regimes (0.05–0.2 mg/kg/day). Plasma samples were collected at predefined times and quantitatively analysed using liquid/liquid extraction followed by reverse phase HPLC with UV‐detection. Meloxicam plasma concentration data were analysed using the population pharmacokinetic approach (software: NONMEM). The final model was used to simulate different dosage regimes. The plasma concentration–time profiles of meloxicam in cats after oral single and multiple dose administration were best described by an open one‐compartment model with first‐order absorption and first‐order elimination. Pharmacokinetic parameters were estimated to be 0.00656 L/h/kg for the total apparent body clearance (CL/F), 0.245 L/kg for the apparent volume of distribution (V/F), 1.26 1/h for the absorption constant (K_A) and 25.7 h for the mean plasma terminal half‐life. Simulations showed that the median trough steady‐state concentrations of 228 ng/mL were reached after five, one or 6 days following a single initial dose of 0.05, 0.1 and 0.2 mg/kg each followed by 0.05 mg/kg/day.     

Effects of soil disturbance on weed seedling emergence and its long-term decline

The long-term effect of different depths of soil cultivation on weed seedling emergence from naturally occurring populations of weed seeds in the soil was examined in four experiments on land previously in pasture, raspberry canes or intensive vegetable production. At approximately monthly intervals, weed seedlings were counted and then killed with contact herbicides, after which plots were cultivated to 250 or 10mm, or were left undisturbed. The treatments were continued for 7 years. One experiment was then discontinued whilst the previously uncultivated plots on the other three were cultivated to 150 mm at approximately monthly intervals for a further 4 years in one experiment, and for 8 years in the other two. After the first year, very few seedlings emerged in the uncultivated and shallow cultivated plots, and seedling numbers declined slowly in the deep-cultivated plots. Under repeated deep cultivation, seedling emergence of almost all species declined exponentially. Different species declined at different rates, with Rubus idaeus L., Plantago lanceolata L., Veronica arvensis L. and Ranunculus spp. being the most rapidly declining group. Rates of decline for individual species were similar to those observed in Europe.Juncus bufonius L. behaved differently from the other species, and showed no decline in seedling numbers. In the initial 7-year period, 28 000 weed seedlings per m^?2 emerged from the deep-cultivated plots on soil previously cropped with vegetables. Over the same period, less than 11 000 seedlings emerged in shallow-cultivated plots, and just over 4000 in uncultivated plots. In the second phase of the experiments, fewer seedlings of most species emerged than in the first phase, and the decline in numbers of Coronpous didymus (L.) Sm. seedlings was slower. Résumé Les effets à long terme de différentes profondeurs de travail du sol sur la levée des mauvaises herbes ont étéétudiés sur des populations naturelles dans des parcelles dont les précédents étaient: paturage, framboisier ou maraichage intensif. À des intervalles d'environ un mois, les jeunes plantes de mauvaises herbes étaient dénombrées puis détruites à l'aide d'herbicides de contact, aprés quoi les parcelles étaient travaillées sur 250 ou 10 mm, ou laissées sans intervention. Cette premiére phase a duré 7 ans. Une expérience a alors été arretée et les parcelles précédemment non cultivées des trois autres ont été travaillées à une profondeur 150 mm, à des intervalles d'environ un mois pendant 4 ans dans un expérience, et pendant 8 ans dans les deux autres. Aprés un an, trés peu de mauvaises herbes levaient dans les parcelles non cultivés et dans celles travaillées superficiellement, et le nombre de levées diminuait lentement dans les parcelles travaillées profondément. Lá oú le travail profond était répété, les levées de presque toutes les especes declinaient exponentiellement. Les différentes espéces déclinaient à des vitesses différentes,Rubus idaeus L., Plantago lanceolata L., Veronica arvensis L. et Ranunculus spp. déclinant le plus rapidement. Les vitesses de diminution pour les differentes espéces étaient similaires à celles observées en Europe. Juncus bufonius L. se comportait différemment des autres espéces et ne montrait aucune décroissance du nombre de levées. Au cours de la période initiale de 7 ans, 28 000 mauvaises herbes par m^?2 levaient dans les parcelles maraicherés travaillées profondément. Au cours de la meme periode, moins de 11000 mauvaises herbes lavaient dans les parcelles travaillées superficiellement et un peu plus de 4000 dans les parcelles non travaillées. Dans la seconde phase de I'expérience, on observait moins de levées de la plupart des especes que au cours de la premiére et la decroissance du nombre de levés de Coronpous didymus (L.) Sm. était moins rapide. Einfluβ der Bodenbearbeitung auf Keimung und Populationsdynamik von Unkrautern Der langfristige Einfluβ verschieden tiefer Bodenbearbeitung auf die Keimung von Unkrautern aus der naturlich gegebenen Samenbank im Boden wurde in 4 Versuchen auf Flachen untersucht, die vorher als Weide oder mit Himbeer oder intensiven Gemusekulturen genutzt worden waren. Die Keimpflanzen wurden 7 Jahre lang etwa monatlich ausgezahlt und mit Kontaktherbiziden abgetotet, danach wurden die Parzellen 25 tief 15 cm, tief oder gar nicht bearbeitet. Ein Versuch wurde beendet, wahrend eine der 3 ubrigen unbearbeiteten Parzellen fur weitere 4 Jahre und die anderen beiden fur weitere 8 Jahre in etwa monatlichen Abstanden 15 cm tief bearbeitet wurden. Am Ende des ersten Jahres liefen auf den unbearbeiteten und den flach bearbeiteten Flachen sehr wenige Keimpflanzen auf; auf den tief bearbeiteten Flachen nahm die Zahl der Keimpflanzen langsam ab. Bei wiederholt tiefer Bodenbearbeitung verringerte sich die Zahl der Keimpflanzen fast aller Arten exponentiell. Am schnellsten sank die Keimrate bei Rubus idaeus L., Plantago lanceolata L., Veronica arvensis L. und Ranunculus spp. Die Abnahme der Keimrate war bei den einzelnen Arten ahnlich wie in Europa beobachtet. Juncus bufonius L. verhielt sich von den anderen Arten abweichend und lieβ keine Abnahme der Keimrate erkennen. In der anfanglichen 7-Jahres-Periode keimten auf den vorher gemusebaulich genutzten, tief bearbeiteten Flachen 28000, den flach bearbeiteten weniger als 11 000 und den unbearbeiten gut 4000 Samen m^?2. In der 2. Versuchsphase wurden bei denmeisten Arten weniger Keimpflanzen als in der 1. beobachtet, und die Abnahme der Keimrate von Coronopus didymus (L). Sm. war langsamer.