Grassland management and conversion into grassland: effects on soil carbon

Grasslands are heavily relied upon for food and forage production. A key component for sustaining production in grassland ecosystems is the maintenance of soil organic matter (SOM), which can be strongly influenced by management. Many management techniques intended to increase forage production may potentially increase SOM, thus sequestering atmospheric carbon (C). Further, conversion from either cultivation or native vegetation into grassland could also sequester atmospheric carbon. We reviewed studies examining the influence of improved grassland management practices and conversion into grasslands on soil C worldwide to assess the potential for C sequestration. Results from 115 studies containing over 300 data points were analyzed. Management improvements included fertilization (39%), improved grazing management (24%), conversion from cultivation (15%) and native vegetation (15%), sowing of legumes (4%) and grasses (2%), earthworm introduction (1%), and irrigation (1%). Soil C content and concentration increased with improved management in 74% of the studies, and mean soil C increased with all types of improvement. Carbon sequestration rates were highest during the first 40 yr after treatments began and tended to be greatest in the top 10 cm of soil. Impacts were greater in woodland and grassland biomes than in forest, desert, rain forest, or shrubland biomes. Conversion from cultivation, the introduction of earthworms, and irrigation resulted in the largest increases. Rates of C sequestration by type of improvement ranged from 0.11 3.04 Mg C.ha(-1) yr(-1), with a mean of 0.54 Mg C.ha(-1).yr(-1) and were highly influenced by biome type and climate. We conclude that grasslands can act as a significant carbon sink with the implementation of improved management.

An analytical solution for diffusion and nonlinear uptake of oxygen in a spherical cell

We develop a new analytical solution for a reactive transport model that describes the steady-state distribution of oxygen subject to diffusive transport and nonlinear uptake in a sphere. This model was originally reported by Lin (Journal of Theoretical Biology, 1976 v60, pp449–457) to represent the distribution of oxygen inside a cell and has since been studied extensively by both the numerical analysis and formal analysis communities. Here we extend these previous studies by deriving an analytical solution to a generalized reaction-diffusion equation that encompasses Lin’s model as a particular case. We evaluate the solution for the parameter combinations presented by Lin and show that the new solutions are identical to a grid-independent numerical approximation.

The accuracy of a new system for estimating organ volume using ultrasound

A new system is described for estimating volume from a series of multiplanar 2D ultrasound images. Ultrasound images are captured using a personal computer video digitizing card and an electromagnetic localization system is used to record the pose of the ultrasound images. The accuracy of the system was assessed by scanning four groups of ten cadaveric kidneys on four different ultrasound machines. Scan image planes were oriented either radially, in parallel or slanted at 30 C to the vertical. The cross-sectional images of the kidneys were traced using a mouse and the outline points transformed to 3D space using the Fastrak position and orientation data. Points on adjacent region of interest outlines were connected to form a triangle mesh and the volume of the kidneys estimated using the ellipsoid, planimetry, tetrahedral and ray tracing methods. There was little difference between the results for the different scan techniques or volume estimation algorithms, although, perhaps as expected, the ellipsoid results were the least precise. For radial scanning and ray tracing, the mean and standard deviation of the percentage errors for the four different machines were as follows: Hitachi EUB-240, −3.0 ± 2.7%; Tosbee RM3, −0.1 ± 2.3%; Hitachi EUB-415, 0.2 ± 2.3%; Acuson, 2.7 ± 2.3%.

In vitro estimation of foetal liver volume using ultrasound, x-ray computed tomography and magnetic resonance imaging

Sixteen formalin-fixed foetal livers were scanned in vitro using a new system for estimating volume from a sequence of multiplanar 2D ultrasound images. Three different scan techniques were used (radial, parallel and slanted) and four volume estimation algorithms (ellipsoid, planimetry, tetrahedral and ray tracing). Actual liver volumes were measured by water displacement. Twelve of the sixteen livers also received x-ray computed tomography (CT) and magnetic resonance (MR) scans and the volumes were calculated using voxel counting and planimetry. The percentage accuracy (mean ± SD) was 5.3 ± 4.7%, −3.1 ± 9.6% and −0.03 ± 9.7% for ultrasound (radial scans, ray volumes), MR and CT (voxel counting) respectively. The new system may be useful for accurately estimating foetal liver volume in utero.

Phase III study of afatinib or cisplatin plus pemetrexed in patients with metastatic lung adenocarcinoma with EGFR mutations

Purpose The LUX-Lung 3 study investigated the efficacy of chemotherapy compared with afatinib, a selective, orally bioavailable ErbB family blocker that irreversibly blocks signaling from epidermal growth factor receptor (EGFR/ErbB1), human epidermal growth factor receptor 2 (HER2/ErbB2), and ErbB4 and has wide-spectrum preclinical activity against EGFR mutations. A phase II study of afatinib in EGFR mutation-positive lung adenocarcinoma demonstrated high response rates and progression-free survival (PFS). Patients and Methods In this phase III study, eligible patients with stage IIIB/IV lung adenocarcinoma were screened for EGFR mutations. Mutation-positive patients were stratified by mutation type (exon 19 deletion, L858R, or other) and race (Asian or non-Asian) before two-to-one random assignment to 40 mg afatinib per day or up to six cycles of cisplatin plus pemetrexed chemotherapy at standard doses every 21 days. The primary end point was PFS by independent review. Secondary end points included tumor response, overall survival, adverse events, and patient-reported outcomes (PROs). Results A total of 1,269 patients were screened, and 345 were randomly assigned to treatment. Median PFS was 11.1 months for afatinib and 6.9 months for chemotherapy (hazard ratio [HR], 0.58; 95% CI, 0.43 to 0.78; P = .001). Median PFS among those with exon 19 deletions and L858R EGFR mutations (n = 308) was 13.6 months for afatinib and 6.9 months for chemotherapy (HR, 0.47; 95% CI, 0.34 to 0.65; P = .001). The most common treatmentrelated adverse events were diarrhea, rash/acne, and stomatitis for afatinib and nausea, fatigue, and decreased appetite for chemotherapy. PROs favored afatinib, with better control of cough, dyspnea, and pain. Conclusion Afatinib is associated with prolongation of PFS when compared with standard doublet chemotherapy in patients with advanced lung adenocarcinoma and EGFR mutations.

Regulation of P-fimbrial phase variation frequencies in Escherichia coli CFT073

Adherence of uropathogenic Escherichia coli to host tissue is required for infection and is mediated by fimbriae, such as pyelonephritis-associated pili (Pap). Expression of P fimbriae is regulated by phase variation, and to date, phase transition frequencies have been measured only for pap regulatory region constructs integrated into the E. coli K-12 chromosome. The aim of this work was to measure P phase transition frequencies in clinical isolates for the first time, including frequencies for the sequenced strain E. coli CFT073. P fimbriation and associated phase transition frequencies were measured for two E. coli clinical isolates and compared with levels for homologous pap constructs in E. coli K-12. Fimbriation and off-to-on transition frequencies were always higher in the clinical isolate. It was concluded that the regulatory inputs controlling papI expression are likely to be different in E. coli CFT073 and E. coli K-12 as (i) phase variation could be stimulated in E. coli K-12 by induction of papI and (ii) the level of expression of a papI::gfp+ fusion was higher in E. coli CFT073 than in E. coli K-12. Furthermore, phase transition frequencies for the two E. coli CFT073 pap clusters were shown to be different depending on the culture conditions, indicating that there is a hierarchy of expression depending on signal inputs.

Machine learning for activity recognition : hip versus wrist data

Problem addressed Wrist-worn accelerometers are associated with greater compliance. However, validated algorithms for predicting activity type from wrist-worn accelerometer data are lacking. This study compared the activity recognition rates of an activity classifier trained on acceleration signal collected on the wrist and hip. Methodology 52 children and adolescents (mean age 13.7 +/- 3.1 year) completed 12 activity trials that were categorized into 7 activity classes: lying down, sitting, standing, walking, running, basketball, and dancing. During each trial, participants wore an ActiGraph GT3X+ tri-axial accelerometer on the right hip and the non-dominant wrist. Features were extracted from 10-s windows and inputted into a regularized logistic regression model using R (Glmnet + L1). Results Classification accuracy for the hip and wrist was 91.0% +/- 3.1% and 88.4% +/- 3.0%, respectively. The hip model exhibited excellent classification accuracy for sitting (91.3%), standing (95.8%), walking (95.8%), and running (96.8%); acceptable classification accuracy for lying down (88.3%) and basketball (81.9%); and modest accuracy for dance (64.1%). The wrist model exhibited excellent classification accuracy for sitting (93.0%), standing (91.7%), and walking (95.8%); acceptable classification accuracy for basketball (86.0%); and modest accuracy for running (78.8%), lying down (74.6%) and dance (69.4%). Potential Impact Both the hip and wrist algorithms achieved acceptable classification accuracy, allowing researchers to use either placement for activity recognition.

Does the technique employed for skin temperature assessment alter outcomes? A systematic review

Skin temperature is an important physiological measure that can reflect the presence of illness and injury as well as provide insight into the localised interactions between the body and the environment. The aim of this systematic review was to analyse the agreement between conductive and infrared means of assessing skin temperature which are commonly employed in in clinical, occupational, sports medicine, public health and research settings. Full-text eligibility was determined independently by two reviewers. Studies meeting the following criteria were included in the review: 1) the literature was written in English, 2) participants were human (in vivo), 3) skin surface temperature was assessed at the same site, 4) with at least two commercially available devices employed—one conductive and one infrared—and 5) had skin temperature data reported in the study. A computerised search of four electronic databases, using a combination of 21 keywords, and citation tracking was performed in January 2015. A total of 8,602 were returned. Methodology quality was assessed by 2 authors independently, using the Cochrane risk of bias tool. A total of 16 articles (n = 245) met the inclusion criteria. Devices are classified to be in agreement if they met the clinically meaningful recommendations of mean differences within ±0.5 °C and limits of agreement of ±1.0 °C. Twelve of the included studies found mean differences greater than ±0.5 °C between conductive and infrared devices. In the presence of external stimulus (e.g. exercise and/or heat) five studies foundexacerbated measurement differences between conductive and infrared devices. This is the first review that has attempted to investigate presence of any systemic bias between infrared and conductive measures by collectively evaluating the current evidence base. There was also a consistently high risk of bias across the studies, in terms of sample size, random sequence generation, allocation concealment, blinding and incomplete outcome data. This systematic review questions the suitability of using infrared cameras in stable, resting, laboratory conditions. Furthermore, both infrared cameras and thermometers in the presence of sweat and environmental heat demonstrate poor agreement when compared to conductive devices. These findings have implications for clinical, occupational, public health, sports science and research fields.

Novel TBK1 truncating mutation in a familial amyotrophic lateral sclerosis patient of Chinese origin

Missense and frameshift mutations in TRAF family member-associated NF-kappa-B activator (TANK)-binding kinase 1 (TBK1) have been reported in European sporadic and familial amyotrophic lateral sclerosis (ALS) cohorts. To assess the role of TBK1 in ALS patient cohorts of wider ancestry, we have analyzed whole-exome sequence data from an Australian cohort of familial ALS (FALS) patients and controls. We identified a novel TBK1 deletion (c.1197delC) in a FALS patient of Chinese origin. This frameshift mutation (p.L399fs) likely results in a truncated protein that lacks functional domains required for adapter protein binding, as well as protein activation and structural integrity. No novel or reported TBK1 mutations were identified in FALS patients of European ancestry. This is the first report of a TBK1 mutation in an ALS patient of Asian origin and indicates that sequence variations in TBK1 are a rare cause of FALS in Australia. © 2015 Elsevier Inc.