Missing value estimation for DNA microarray gene expression data: local least squares imputation

In our article, only a set of random positions of missing valueswas used for each dataset. However, imputation methods may     

Multiplex Cytological Profiling Assay to Measure Diverse Cellular States

Computational methods for image-based profiling are under active development, but their success hinges on assays that can capture a wide range of phenotypes. We have developed a multiplex cytological profiling assay that “paints the cell” with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar  annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.     

The rate of O₂ loss from mesenteric arterioles is not unusually high

The O(2) disappearance curve (ODC) recorded in an arteriole after the rapid arrest of blood flow reflects the complex interaction among the dissociation of O(2) from hemoglobin, O(2) diffusivity, and rate of respiration in the vascular wall and surrounding tissue. In this study, the analysis of experimental ODCs allowed the estimation of parameters of O(2) transport and O(2) consumption in the microcirculation of the mesentery. We collected ODCs from rapidly arrested blood inside rat mesenteric arterioles using scanning phosphorescence quenching microscopy (PQM). The technique was used to prevent the artifact of accumulated O(2) photoconsumption in stationary media. The observed ODC signatures were close to linear, in contrast to the reported exponential decline of intra-arteriolar Po(2). The rate of Po(2) decrease was 0.43 mmHg/s in 20-μm-diameter arterioles. The duration of the ODC was 290 s, much longer than the 12.8 s reported by other investigators. The arterioles associated with lymphatic microvessels had a higher O(2) disappearance rate of 0.73 mmHg/s. The O(2) flux from arterioles, calculated from the average O(2) disappearance rate, was 0.21 nl O(2)·cm(-2)·s(-1), two orders of magnitude lower than reported in the literature. The physical upper limit of the O(2) consumption rate by the arteriolar wall, calculated from the condition that all O(2) is consumed by the wall, was 452 nl O(2)·cm(-3)·s(-1). From consideration of the microvascular tissue volume fraction in the rat mesentery of 6%, the estimated respiration rate of the vessel wall was ～30 nl O(2)·cm(-3)·s(-1). This result was three orders of magnitude lower than the respiration rate in rat mesenteric arterioles reported by other investigators. Our results demonstrate that O(2) loss from mesenteric arterioles is small and that the O(2) consumption by the arteriolar wall is not unusually large.     

Propagated fixed-bed mixed-acid fermentation: Part I: Effect of volatile solid loading rate and agitation at high pH

Countercurrent fermentation is a high performing process design for mixed-acid fermentation. However, there are high operating costs associated with moving solids, which is an integral component of this configuration. This study investigated the effect of volatile solid loading rate (VSLR) and agitation in propagated fixed-bed fermentation, a configuration which may be more commercially viable. To evaluate the role of agitation on fixed-bed configuration performance, continuous mixing was compared with periodic mixing. VSLR was also varied and not found to affect acid yields. However, increased VSLR and liquid retention time did result in higher conversions, productivity, acid concentrations, but lower selectivities. Agitation was demonstrated to be important for this fermentor configuration, the periodically-mixed fermentation had the lowest conversion and yields. Operating at a high pH (～9) contributed to the high selectivity to acetic acid, which might be industrially desirable but at the cost of lower yield compared to a neutral pH.     

Label free and amplified detection of cancer marker EBNA-1 by DNA probe based biosensors

Epstein-Barr virus (EBV) is a human herpes virus that has been associated with several malignancies as Burkitt's lymphoma, nasopharyngeal carcinoma and Hodgkin's disease. All EBV associated malignancies showed a distinct viral gene expression pattern, while Epstein-Barr nuclear antigen 1 (EBNA-1) is constitutively expressed in all such disorders. Here, the development of a biosensor to detect EBNA-1 protein is reported, which was based on a nucleic acid bioreceptor and a quartz crystal microbalance with a dissipation monitoring (QCM-D) transducer. The DNA probe for EBNA-1 detection was designed and synthesized to mimic its palindromic target sites in the EBV genome. This DNA probe was immobilized on the Au-surface of a QCM-D electrode, followed by the blocking of the accessible Au-surface with 6-mercapto-1-hexanol (6-MHO). The system showed a limit of detection of 50 ng/mL in direct detection of EBNA-1, however, the sensitivity was improved by 2 orders of magnitude (0.5 ng/mL) when an amplification cascade, employing antibodies labeled with alkaline phosphatase (AP), was applied to the system.     

Investigating ADAMTS-mediated aggrecanolysis in mouse cartilage

Proteolysis of the cartilage proteoglycan aggrecan is a feature of arthritis. We present a method for analyzing aggrecanolysis in in vitro cultures of 3-week-old mouse femoral head cartilage based on traditional methods developed for large animal species. Investigators can choose either a simple analysis that detects several aggrecan fragments released into culture medium only or a more comprehensive study that detects all fragments present in both the medium and the cartilage matrix. The protocol comprises (i) cartilage culture and optional cartilage extraction, (ii) a quick and simple colorimetric assay for quantitating aggrecan and (iii) neoepitope western blotting to identify specific aggrecan fragments partitioning to the medium or cartilage compartments. The crucial difference between the methods for mice and larger animals is that the proportion of aggrecan in a given sample is normalized to total aggrecan rather than to tissue wet weight. This necessary break from tradition arises because tiny volumes of liquid clinging to mouse cartilage can increase the apparent tissue wet weight, causing unacceptable errors. The protocol has broad application for the in vitro analysis of transgenic mice, particularly those with mutations that affect cartilage remodeling, arthritic disease and skeletal development. The protocol is robust, reliable and takes 7-11 d to complete.