An undergraduate system-on-chip (SoC) course for computer engineering students

The authors have developed a senior-level undergraduate system-on-chip (SoC) course at San Jose State University, San Jose, CA, that emphasizes SoC design methods and hardware-software codesign techniques. The course uses a "real world" design project as the teaching vehicle and implements an SoC platform to control a five-axis robotic arm using Altera's state-of-the-art Excalibur chip. The Excalibur chip contains both ARM Corporation's embedded processor and a programmable logic device (PLD) array. The course goes through a complete hardware-software codesign flow from implementing custom hardware devices on a PLD to developing an embedded algorithm in a state-of-the-art design environment for a complete SoC solution. Students learn the Quartus II design environment by examining the sample design files in Altera's EXPA1 development kit and following the step-by-step instructions toward creating a simple embedded application. After this familiarization process, students define the architectural specifications of a memory-mapped servo controller, implement it in the Excalibur's PLD array, and interface this device with the ARM processor's internal bus to control each robotic arm servo. Functional regression tests and post-synthesis timing verification steps are applied to the servo controller following the implementation phase. Subsequently, students integrate the servo controller with the rest of the system and perform board-level functional verification tests to observe whether the robotic arm can move an object from a source to a destination point accurately. Students also develop an embedded algorithm, which translates user inputs in Cartesian coordinates into robotic arm movements in spherical coordinates during laboratory sessions.     

Three public enemies: cut, copy, and paste

Many software developers know the feeling of desperately debugging a program only to discover after a sleepless night that the error stemmed from copy-pasted code segments that had become inconsistent in subsequent editing. The problems arising from copied code are not new, and many researchers have investigated how to automatically find copied code segments. Given the extensive use of copy-paste operations and their tendency to cause inconsistencies, there is clearly a pressing need to rethink current editor programs. One solution is to replace cut, copy, and paste with operations that correspond directly to the intended semantics behind their use. With these operations, the user can specify semantic relationships among copied objects, and the editor program can use that information to help in the long-term support of those relationships. It would thus avoid the inconsistencies that currently arise from the use of cut, copy, and paste.     

Automation for High-throughput Identification and Picking of GFP Expressing Colonies

Green fluorescent protein (GFP) has many applications as a marker in living cells, and has become widely used as a reporter gene in microbial, plant and animal cells. Screening microbial colonies for GFP expression enables various types of assays (e.g. for secretory mutations). However, this is laborious, non-quantitative and potentially hazardous to the operator (due to UV illumination) when performed manually. In order to address this the GloPix robot was developed. The imaging system discriminates between colonies based on the level of fluorescence activity and the picking function automatically transfers cells to microplate wells. Measuring fluorescent activity allows quantitation of fluorescent tag concentration/expression.     

Measurement of dilute 29Si species in solution using a large volume coil and DEFT NMR

A large-sample-volume nuclear magnetic resonance (NMR) spectroscopy probehead has been developed for the detection and characterization of low concentrations of 29Si species in aqueous solution. The approach described entails the use of a large-diameter radio frequency solenoid coil that permits substantially larger sample volumes to be investigated at moderate magnetic field strengths, compared with conventional NMR probehead configurations. In addition, difficulties presented by long 29Si T1 relaxation times have been circumvented by using the DEFT NMR pulse sequence, which permits more rapid signal averaging. Through a combination of these hardware and methodological improvements, high-resolution 29Si NMR spectra have been obtained at 4.2 T (29Si resonance frequency = 36.8 MHz) for an 800 microM solution of 96% 29Si-enriched silicic acid, H4SiO4 (pH approximately 8), with a signal-to-noise ratio of 16 and a line width of 31 Hz after 3 h of total measurement time.     

Cartilage degeneration in relation to repetitive pressure: case study of a unilateral hip hemiarthroplasty patient

The mitochondrial, inner-membrane-associated, reversible NADPH-->NAD transhydrogenase of adult Hymenolepis diminuta physiologically couples matrix-localized, NADP-specific "malic" enzyme with NADH-dependent anaerobic electron transport. Employing submitochondrial particles (SMP) as the source of enzyme activity and both spectrophotometric and fluorometric assessments, the present study made evident that in its catalysis of transhydrogenation between NADPH and NAD, the cestode enzyme engages in the concomitant transmembrane translocation of protons. As assessed spectrophotometrically, the catalysis of NADPH-dependent NAD reduction by H. diminuta SMP was stimulated significantly by carbonyl cyanide 3-chlorophenylhydrazone (CCCP), carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP), as well as by the protonophoric anthelmintic, niclosamide. In addition, N,N'-dicyclohexylcarbodiimide (DCCD) markedly diminished SMP-catalyzed hydride ion transfer between NADPH and NAD. The catalysis by SMP of concomitant, transhydrogenase-mediated proton translocation was evaluated more directly via fluorometric assays using 8-anilino-1-napthalenesulfonic acid (ANS) as the probe. These latter evaluations revealed a transhydrogenase-dependent enhancement of ANS fluorescence in accord with an intravesicular accumulation of protons. ANS fluorescence was quenched rapidly when the assay system was supplemented with CCCP, FCCP, or niclosamide. Consistent with the helminth transhydrogenase acting as a proton pump, transhydrogenase-mediated enhanced fluorescence also was inhibited by DCCD. Considered collectively, these data indicated, apparently for the first time for any invertebrate system, that the transhydrogenase, in catalyzing the NADPH-->NAD reaction, acts in the translocation of protons from the matrix to the intermembrane space mitochondrial compartment.     

In vivo neurochemistry of the brain in schizophrenia as revealed by magnetic resonance spectroscopy

Magnetic resonance spectroscopy (MRS), an application of the methods of nuclear magnetic resonance (NMR), is a functional imaging modality that provides a view of localized biochemistry in vivo. A number of studies applying MRS to the neurochemistry of schizophrenia have been reported, which encompass a range of patient populations, states of medication, anatomic regions, nuclear species, and MRS techniques. A brief review of the history and methodology of NMR and MRS is presented. Comparison is made of MRS capabilities with other functional imaging modalities. Aspects of the neurochemistry of schizophrenia relevant to MRS studies are reviewed, as are the reported MRS studies involving patients with schizophrenia. Areas of consistent findings include decreased phosphomonoesters and increased phosphodiesters in frontal lobes, and decreases in the putative neuronal cell marker, N-acetylaspartate, in temporal lobes. Studies of neurotransmitters such as glutamate, gamma-aminobutyric acid, and glutamine have generated inconsistent results. New insights into alterations in neurochemistry in schizophrenia have been provided by MRS. Studies of neurotransmitters have future potential with improvements in field strength and in spectral editing techniques. MRS has the potential to measure brain medication levels and simultaneous effects on neurochemistry. MRS may assist in characterizing high-risk populations, and ultimately guide medication use.     

Laminaria augmentation of midtrimester pregnancy termination by intramuscular prostaglandin 15 (S) 15-methyl F2 alpha

A group of 15 midtrimester gravid patients underwent intracervical laminaria tent insertion prior to repeated intramuscular injections of 250mu g of prostaglandin 15 (S) 15-methyl F2 alpha at two-hour intervals for elective termination of pregnancy. This group was compared with a previously reported group of 80 patients who had received identical treatment without laminaria insertion. A significant reduction in mean abortion time and an increased 24-hour abortion rate were observed with the addition of laminaria. There was a proportionate decrease in gastrointestinal side effects as well as a reduced need for analgesia in the laminaria group with no complications attributable to the laminaria insertion.