Data-analysis strategies for image-based cell profiling

Image-based cell profiling is a high-throughput strategy for the quantification of phenotypic differences among a variety of cell populations. It paves the way to studying biological systems on a large scale by using chemical and genetic perturbations. The general workflow for this technology involves image acquisition with high-throughput microscopy systems and subsequent image processing and analysis. Here, we introduce the steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images. We recommend techniques that have proven useful in each stage of the data analysis process, on the basis of the experience of 20 laboratories worldwide that are refining their image-based cell-profiling methodologies in pursuit of biological discovery. The recommended techniques cover alternatives that may suit various biological goals, experimental designs, and laboratories' preferences.Peer reviewe

Differences in acoustic impedance of fresh and embedded human trabecular bone samples - Scanning acoustic microscopy and numerical evaluation

Trabecular bone samples are traditionally embedded and polished for scanning acoustic microscopy (SAM). The effect of sample processing, including dehydration, on the acoustic impedance of bone is unknown. In this study, acoustic impedance of human trabecular bone samples (n = 8) was experimentally assessed before (fresh) and after embedding using SAM and two-dimensional (2-D) finite-difference time domain simulations. Fresh samples were polished with sandpapers of different grit (P1000, P2500, and P4000). Experimental results indicated that acoustic impedance of samples increased significantly after embedding [mean values 3.7 MRayl (fresh), 6.1 MRayl (embedded), p < 0.001]. After polishing with different papers, no significant changes in acoustic impedance were found, even though higher mean values were detected after polishing with finer (P2500 and P4000) papers. A linear correlation (r = 0.854, p < 0.05) was found between the acoustic impedance values of embedded and fresh bone samples polished using P2500 SiC paper. In numerical simulations dehydration increased the acoustic impedance of trabecular bone (38%), whereas changes in surface roughness of bone had a minor effect on the acoustic impedance (-1.56%/0.1 μm). Thereby, the numerical simulations corroborated the experimental findings. In conclusion, acoustic impedance measurement of fresh trabecular bone is possible and may provide realistic material values similar to those of living bone

Finite difference time domain model of ultrasound propagation in agarose scaffold containing collagen or chondrocytes

Measurement of ultrasound backscattering is a promising diagnostic technique for arthroscopic evaluation of articular cartilage. However, contribution of collagen and chondrocytes on ultrasound backscattering and speed of sound in cartilage is not fully understood and is experimentally difficult to study. Agarose hydrogels have been used in tissue engineering applications of cartilage. Therefore, the aim of this study was to simulate the propagation of high frequency ultrasound (40 MHz) in agarose scaffolds with varying concentrations of chondrocytes (1 to 32 × 10 cells/ml) and collagen (1.56-200 mg/ml) using transversely isotropic two-dimensional finite difference time domain method (FDTD). Backscatter and speed of sound were evaluated from the simulated pulse-echo and through transmission measurements, respectively. Ultrasound backscatter increased with increasing collagen and chondrocyte concentrations. Furthermore, speed of sound increased with increasing collagen concentration. However, this was not observed with increasing chondrocyte concentrations. The present study suggests that the FDTD method may have some applicability in simulations of ultrasound scattering and propagation in constructs containing collagen and chondrocytes. Findings of this study indicate the significant role of collagen and chondrocytes as ultrasound scatterers and can aid in development of modeling approaches for understanding how cartilage architecture affects to the propagation of high frequency ultrasound

Characterizing human subchondral bone properties using near-infrared (NIR) spectroscopy

Degenerative joint conditions are often characterized by changes in articular cartilage and subchondral bone properties. These changes are often associated with subchondral plate thickness and trabecular bone morphology. Thus, evaluating subchondral bone integrity could provide essential insights for diagnosis of joint pathologies. This study investigates the potential of optical spectroscopy for characterizing human subchondral bone properties. Osteochondral samples (n = 50) were extracted from human cadaver knees (n = 13) at four anatomical locations and subjected to NIR spectroscopy. The samples were then imaged using micro-computed tomography to determine subchondral bone morphometric properties, including: plate thickness (Sb.Th), trabecular thickness (Tb.Th), volume fraction (BV/TV), and structure model index (SMI). The relationship between the subchondral bone properties and spectral data in the 1 (650-950 nm), 2 (1100-1350 nm) and 3 (1600-1870 nm) optical windows were investigated using partial least squares (PLS) regression multivariate technique. Significant correlations (p < 0.0001) and relatively low prediction errors were obtained between spectral data in the 1 optical window and Sb.Th (R = 92.3%, error = 7.1%), Tb.Th (R = 88.4%, error = 6.7%), BV/TV (R = 83%, error = 9.8%) and SMI (R = 79.7%, error = 10.8%). Thus, NIR spectroscopy in the 1 tissue optical window is capable of characterizing and estimating subchondral bone properties, and can potentially be adapted during arthroscopy

Phased-array ultrasound technology enhances accuracy of dual frequency ultrasound measurements – towards improved ultrasound bone diagnostics

<p>Overlying soft tissues attenuate ultrasound backscattered from bone, complicating diagnostics of osteoporosis at the most important fracture sites. Dual-frequency ultrasound technique (DFUS) has been proposed to solve this problem through determination of thickness and composition of overlying soft tissue. This study applies DFUS technique for the first time with a phased-array transducer to investigate if the thickness of two interfering layers (oil and water) can be accurately determined in a variety of configurations. Results indicate that DFUS may be used with phased-array ultrasound systems, making them a suitable combination to consider in future development of clinical <i>in vivo</i> ultrasound methodologies.</p

An Economic Analysis of Dismissal Legislation: Determinants of Severance Pay in West Germany

Severance pay is a vital part of employment protection legislation (EPL). We investigate the incidence and level of severance pay for dismissed employees. Our theoretical model predicts that not only the law and its interpretation by labour courts but also the costs of a suit have an impact. Using West German panel data for 1991-2006, we find that the employees' costs resulting from a suit and the legal determinants of such transfers affect the incidence of severance payments. In contrast, their level only varies with legal regulations. Our results imply that the strictness of EPL in Germany varies with extra-legal factors like employees' financial constraints

Reduced Cancer Incidence in Huntington's Disease: Analysis in the Registry Study

Background: People with Huntington's disease (HD) have been observed to have lower rates of cancers. Objective: To investigate the relationship between age of onset of HD, CAG repeat length, and cancer diagnosis. Methods: Data were obtained from the European Huntington's disease network REGISTRY study for 6540 subjects. Population cancer incidence was ascertained from the GLOBOCAN database to obtain standardised incidence ratios of cancers in the REGISTRY subjects. Results: 173/6528 HD REGISTRY subjects had had a cancer diagnosis. The age-standardised incidence rate of all cancers in the REGISTRY HD population was 0.26 (CI 0.22-0.30). Individual cancers showed a lower age-standardised incidence rate compared with the control population with prostate and colorectal cancers showing the lowest rates. There was no effect of CAG length on the likelihood of cancer, but a cancer diagnosis within the last year was associated with a greatly increased rate of HD onset (Hazard Ratio 18.94, p < 0.001). Conclusions: Cancer is less common than expected in the HD population, confirming previous reports. However, this does not appear to be related to CAG length in HTT. A recent diagnosis of cancer increases the risk of HD onset at any age, likely due to increased investigation following a cancer diagnosis

Clinical and genetic characteristics of late-onset Huntington's disease

Background: The frequency of late-onset Huntington's disease (&gt;59 years) is assumed to be low and the clinical course milder. However, previous literature on late-onset disease is scarce and inconclusive. Objective: Our aim is to study clinical characteristics of late-onset compared to common-onset HD patients in a large cohort of HD patients from the Registry database. Methods: Participants with late- and common-onset (30–50 years)were compared for first clinical symptoms, disease progression, CAG repeat size and family history. Participants with a missing CAG repeat size, a repeat size of ≤35 or a UHDRS motor score of ≤5 were excluded. Results: Of 6007 eligible participants, 687 had late-onset (11.4%) and 3216 (53.5%) common-onset HD. Late-onset (n = 577) had significantly more gait and balance problems as first symptom compared to common-onset (n = 2408) (P &lt;.001). Overall motor and cognitive performance (P &lt;.001) were worse, however only disease motor progression was slower (coefficient, −0.58; SE 0.16; P &lt;.001) compared to the common-onset group. Repeat size was significantly lower in the late-onset (n = 40.8; SD 1.6) compared to common-onset (n = 44.4; SD 2.8) (P &lt;.001). Fewer late-onset patients (n = 451) had a positive family history compared to common-onset (n = 2940) (P &lt;.001). Conclusions: Late-onset patients present more frequently with gait and balance problems as first symptom, and disease progression is not milder compared to common-onset HD patients apart from motor progression. The family history is likely to be negative, which might make diagnosing HD more difficult in this population. However, the balance and gait problems might be helpful in diagnosing HD in elderly patients