MetaMol: high-quality visualization of molecular skin surface

Modeling and visualizing molecular surfaces is an important and challenging task in bioinformatics. Such surfaces play an essential role in better understanding the chemical and physical properties of molecules. However, constructing and displaying molecular surfaces requires complex algorithms. In this article we introduce MetaMol, a new program that generates high-quality images in interactive time. In contrast with existing software that discretizes the surface with triangles or grids, our program is based on a GPU accelerated ray-casting algorithm that directly uses the piecewise-defined algebraic equation of the molecular skin surface. As a result, both better performances and higher quality are obtained.     

Top-down proteomic analysis by MALDI-TOF profiling: Concentration-independent biomarkers

Although numerous protein biomarkers have been correlated with advanced disease states, no new clinical assays have been developed. Goals often anticipate disease-specific protein changes that exceed values among healthy individuals, a property common to acute phase reactants. This review considers somewhat different approaches. It focuses on intact protein isoform ratios that present a biomarker without change in the total concentration of the protein. These will seldom be detected by peptide level analysis or by most antibody-based assays. For example, application of an inexpensive method to large sample groups resulted in observation of several polymorphisms, including the first structural polymorphism of apolipoprotein C1. Isoform distribution of this protein was altered and was eventually linked to increased obesity. Numerous other protein isoforms included C- and N-terminal proteolysis, changes of glycoisoform ratios and certain types of sulfhydryl oxidation. While many of these gave excellent statistical correlation with advanced disease, clinical utility was not apparent. More important may be that protein isoform ratios were very stable in each individual. Diagnosis by longitudinal analysis of the same individual might increase sensitivity of protein biomarkers by 20-fold or more. Protein changes that exceed the range of values found among healthy individuals may be uncommon.     

Roll manufacturing of flexible microfluidic devices in thin PMMA and COC foils by embossing and lamination

Microfluidics on foil is gaining momentum due to a number of advantages of employing thin films combined with the capability of cost-effective high-volume manufacturing of devices. In this work, ultra-thin, flexible Y-microreactors with microchannels of 100 μm width and 30 μm depth were fabricated in thermoplastic polymer foils. The fluidic pattern was hot roll embossed in 125 μm thick poly-methyl-methacrylate (PMMA) and 130 μm thick cyclic-olefin-copolymer (COC) films using a dry-etched microstructured silicon wafer as a flat embossing tool in a laminator. The sealing of the channels was performed with two different techniques, one based on lamination of SU8 dry film resist (DFR) and the other one based on spin-coated poly-dimethylsiloxane (PDMS). Testing of the interconnected microreactor was carried out using two dye colorant solutions to demonstrate mixing.     

Somatosensory Processing and Schizophrenia Liability: Proprioception, Exteroceptive Sensitivity, and Graphesthesia Performance in the Biological Relatives of Schizophrenia Patients.

In the present study, the authors examined somatosensory processing in 30 biological relatives of persons with schizophrenia (hereafter called "schizophrenia relatives"), 30 biological relatives of persons with bipolar affective disorder (psychiatric family control subjects), and 30 healthy control subjects with no family history of psychopathology. All 3 groups completed a weight discrimination task, a 2-point discrimination task, and a complex cognitive somatosensory task (i.e., graphesthesia). The schizophrenia relatives performed significantly worse on all 3 somatosensory tasks compared with both the healthy control subjects and the bipolar relatives. The healthy control subjects and psychiatric family control subjects showed no significant differences on any of the somatosensory tasks. Within the weight discrimination and 2-point discrimination tasks, schizophrenia relatives showed group differences on the d' index, the measure of sensitivity, whereas all 3 groups did not differ on lnβ, the measure of response bias, suggesting a genuine difference in weight and touch sensitivity. The d' value of the weight discrimination task was significantly associated with both the cognitive-perceptual factor and negative symptom factor of the clinical questionnaire (e.g., Schizotypal Personality Questionnaire; SPQ), whereas the 2-point discrimination d' value and graphesthesia scores were significantly associated only with the cognitive-perceptual factor of the SPQ. Implications for the possible relation between somatosensory task performance and schizophrenia liability are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Comparing the effects of text size and format on the readibility of computer-displayed Times New Roman and Arial text

Times New Roman and Arial typefaces in 10- and 12-point, dot-matrix and anti-aliased format conditions were compared for readability (accuracy, reading speed, and accuracy/reading speed), as well as perceptions of typeface legibility, sharpness, ease of reading, and general preference. In assessing readability, the 10-point anti-aliased Arial typeface was read slower than the other type conditions. Examining perceptions of typeface legibility, sharpness, and ease of reading detected significant effects for typeface, size, and format. Overall, the 12-point dot-matrix Arial typeface was preferred to the other typefaces. Recommendations for appropriate typeface combinations for computer-displayed text are discussed.     

Management of imprecision and uncertainty for production activity control

The operational levels of production management, often called production activity control (PAC) or manufacturing process control, require increasing reaction capabilities in order to adapt the workshop management to the changes of its environment. It often implies giving more responsibilities to the low decision levels. However, the management of the corresponding degrees of freedom is generally unusual. In such a situation, decision support systems (DSSs) provide a way to reconcile the satisfaction of mid-level objectives and the reaction requirements. A conceptual model is described that provides a design framework for a PAC DSS. Since the available knowledge lies mainly in expertise, a DSS has been implemented using a knowledge-based system. The uncertainty and imprecision of the managed information led to the use of fuzzy logic as a modeling tool. Moreover, various inference semantics have been implemented in the expert rules because different kinds of reasoning have been identified. Two versions of the DSS are described and several examples of implemented reasoning processes are developed.     

Correlated fluorescence lifetime and spectral measurements in living cells

Studies of proteins' interaction in cells by FRET can take benefit from two important photo-physical properties describing fluorescent proteins: fluorescence emission spectrum and fluorescence lifetime. These properties provide specific and complementary information about the tagged proteins and their environment. However, none of them taken individually can completely quantify the involved fluorophore characteristics due to their multiparametric dependency with molecular environment, experimental conditions, and interpretation complexity. A solution to get a better understanding of the biological process implied at the cellular level is to combine the spectral and temporal fluorescence data acquired simultaneously at every cell region under investigation. We present the SLiM-SPRC160, an original temporal/spectral acquisition system for simultaneous lifetime measurements in 16 spectral channels directly attached to the descanned port of a confocal microscope with two-photon excitation. It features improved light throughput, enabling low-level excitation and minimum invasivity in living cells studies. To guarantee a fairly good level of accuracy and reproducibility in the measurements of fluorescence lifetime and spectra on living cells, we propose a rigorous protocol for running experiments with this new equipment that preserves cell viability. The usefulness of SLiM approach for the precise determination of overlapping fluorophores is illustrated with the study of known solutions of rhodamine. Then, we describe reliable FRET experiments in imaging mode realized in living cells using this protocol. We also demonstrate the benefit of localized fluorescence spectrum-lifetime acquisitions for the dynamic study of fluorescent proteins. proteins.     

An integer goal programming model for determining capital expenditures for correctional facilities

The selection of capital expenditure projects for the construction of state correctional facilities is often complicated by the existence of multiple and conflicting objectives on the part of the various interest groups involved in the decision-making process. While some groups view the limited availability of state funds to construct such facilities as the paramount consideration, others might consider having adequate capacity to house prisoners in a satisfactory manner, and the effect of prison overcrowding on prisoner sentencing as the primary factors in the decision to construct new facilities. As such. it is imperative that the limited funds available for constructing correctional facilities be allocated in the most efficient and satisfactory manner possible. In this paper, integer goal programming is demonstrated via a case example as a means for allocating funds for capital expenditures for new and renovated correctional facilities. Sensitivity analysis is performed using the model in order to demonstrate its capability for testing various planning scenarios including alternative priority structures, goal constraints and goal levels.