Selecting and assessing challenge problems

Abstract

Organisations conducting research programs often focus the work of their scientists and technologists on challenge problems (CPs). These challenges are designed to ensure that progress is measurable and relevant to the goals of the program sponsor. Generating and selecting pertinent CPs is difficult, as is assessing their value. We describe a method of generating and selecting CPs and its application in a highly collaborative, multi-organisation research program. Thirty-eight biologists, chemists, mathematicians and computer scientists across academic, commercial and government organisations generated and ranked their top choices from among 12 richly described candidate challenge problems. A ranked-choice voting formula was applied. Five CPs were highly scored; the remaining seven were distributed across a lower range of scores. The program sponsor subsequently directed researchers to address six CPs, including the elected five. Analysis of the rationales that participants offered for their CP rankings revealed four domain-independent dimensions of value: capability, speed, impact and synergy. These dimensions of value can help managers of interdisciplinary research programs systematically select a portfolio of CPs that will efficiently apply utilise resources towards program goals and facilitate measurement of scientific progress.     

Human brain metabolic response to caffeine and the effects of tolerance

OBJECTIVE: Since there is limited information concerning caffeine's metabolic effects on the human brain, the authors applied a rapid proton echo-planar spectroscopic imaging technique to dynamically measure regional brain metabolic responses to caffeine ingestion. They specifically measured changes in brain lactate due to the combined effects of caffeine's stimulation of glycolysis and reduction of cerebral blood flow. METHOD: Nine heavy caffeine users and nine caffeine-intolerant individuals, who had previously discontinued or substantially curtailed use of caffeinated products because of associated anxiety and discomforting physiological arousal, were studied at baseline and then during 1 hour following ingestion of caffeine citrate (10 mg/kg). To assess state-trait contributions and the effects of caffeine tolerance, five of the caffeine users were restudied after a 1- to 2-month caffeine holiday. RESULTS: The caffeine-intolerant individuals, but not the regular caffeine users, experienced substantial psychological and physiological distress in response to caffeine ingestion. Significant increases in global and regionally specific brain lactate were observed only among the caffeine-intolerant subjects. Reexposure of the regular caffeine users to caffeine after a caffeine holiday resulted in little or no adverse clinical reaction but significant rises in brain lactate which were of a magnitude similar to that observed for the caffeine-intolerant group. CONCLUSIONS: These results provide direct evidence for the loss of caffeine tolerance in the human brain subsequent to caffeine discontinuation and suggest mechanisms for the phenomenon of caffeine intolerance other than its metabolic effects on elevating brain lactate.     

Topology of Euglena chloroplast protein precursors within endoplasmic reticulum to Golgi to chloroplast transport vesicles

Euglena chloroplast protein precursors are transported as integral membrane proteins from the endoplasmic reticulum (ER) to the Golgi apparatus prior to chloroplast localization. All Euglena chloroplast protein precursors have functionally similar bipartite presequences composed of an N-terminal signal peptide domain and a stromal targeting domain containing a hydrophobic region approximately 60 amino acids from the predicted signal peptidase cleavage site. Asparagine-linked glycosylation reporters and presequence deletion constructs of the precursor to the Euglena light-harvesting chlorophyll a/b-binding protein of photosystem II (pLHCPII) were used to identify presequence regions translocated into the ER lumen and stop transfer membrane anchor domains. An asparagine-linked glycosylation site present at amino acid 148 of pLHCPII near the N terminus of mature LHCPII was not glycosylated in vitro by canine microsomes while an asparagine-linked glycosylation site inserted at amino acid 40 was. The asparagine at amino acid 148 was glycosylated upon deletion of amino acids 46-146, which contain the stromal targeting domain, indicating that the hydrophobic region within this domain functions as a stop transfer membrane anchor sequence. Protease protection assays indicated that for all constructs, mature LHCPII was not translocated across the microsomal membrane. Taken together with the structural similarity of all Euglena presequences, these results demonstrate that chloroplast precursors are anchored within ER and Golgi transport vesicles by the stromal targeting domain hydrophobic region oriented with the presequence N terminus formed by signal peptidase cleavage in the vesicle lumen and the mature protein in the cytoplasm.     

The effect of exercise and rehabilitation on anterior-posterior knee displacements after anterior cruciate ligament autograft reconstruction

We studied the effect of rehabilitation strength training and return to activities on anterior-posterior knee displacements after patellar tendon autogenous anterior cruciate ligament reconstruction. A total of 938 measurements were sequentially collected for 142 patients with the KT-2000 arthrometer. Rehabilitation included immediate knee motion and early weightbearing, light sports at 6 months, and competitive sports at 8 months or later. At a minimum of 2 years after surgery, 121 patients (85%) had normal displacements (less than 3 mm of increase at 134 N), 14 (10%) had 3 to 5.5 mm of increase (partial function), and 7 (5%) had more than 5.5 mm of increase (failed). There was no association found between the initial onset of the abnormal displacements in the 21 knees and either the amount of time after surgery or the rehabilitation program. Six of the seven grafts that failed did so in the 1st postoperative year. Serial displacement measurements allow early detection of graft stretching and subsequent modification of rehabilitation or delay in return to strenuous activities. These measurements showed that the rehabilitation program used in this study was not itself injurious and resulted in an acceptable failure rate of 5%.     

Effects of the E177K mutation in D-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity

D-Amino acid transaminase is a bacterial enzyme that uses pyridoxal phosphate (PLP) as a cofactor to catalyze the conversion of D-amino acids into their corresponding alpha-keto acids. This enzyme has already been established as a target for novel antibacterial agents through suicide inactivation by a number of compounds. To improve their potency and specificity, the detailed enzyme mechanism, especially the role of its PLP cofactor, is under investigation. Many PLP-dependent transaminases have a negatively charged amino acid residue forming a salt-bridge with the pyridine nitrogen of its cofactor that promotes its protonation to stabilize the formation of a ketimine intermediate, which is subsequently hydrolyzed in the normal transaminase reaction pathway. However, alanine racemase has a positively charged arginine held rigidly in place by an extensive hydrogen bond network that may destabilize the ketimine intermediate, and make it too short-lived for a transaminase type of hydrolysis to occur. To test this hypothesis, we changed Glu-177 into a titratable, positively charged lysine (E177K). The crystal structure of this mutant shows that the positive charge of the newly introduced lysine side chain points away from the nitrogen of the cofactor, which may be due to electrostatic repulsions not being overcome by a hydrogen bond network such as found in alanine racemase. This mutation makes the active site more accessible, as exemplified by both biochemical and crystallographic data: CD measurements indicated a change in the microenvironment of the protein, some SH groups become more easily titratable, and at pH 9.0 the PMP peak appeared around 315 nm rather than at 330 nm. The ability of this mutant to convert L-alanine into D-alanine increased about 10-fold compared to wild-type and to about the same extent as found with other active site mutants. On the other hand, the specific activity of the E177K mutant decreased more than 1000-fold compared to wild-type. Furthermore, titration with L-alanine resulted in the appearance of an enzyme-substrate quinonoid intermediate absorbing around 500 nm, which is not observed with usual substrates or with the wild-type enzyme in the presence of L-alanine. The results overall indicate the importance of charged amino acid side chains relative to the coenzyme to maintain high catalytic efficiency.     

Tooth stabilization for orthodontic retention

This article reviews stability and retention of the orthodontically treated dentition. Factors and conditions that influence post-treatment stability are discussed. Methods for stabilizing and retaining the occlusion are reviewed.     

Upper tibial hyperextension fractures in infants: another occult toddler''s fracture

Our study describes a newly designed stapedotomy prosthesis which consists of two components: (1) a platinum ribbon, and (2) a Teflon shaft. The first innovation is a flattened 'tab' on the posterior aspect of the platinum ribbon. The second innovation concerns the dual diameter cylinder-like shaft. Our prosthesis was implanted into 25 individuals, who underwent stapedotomy for stapes fixation, and the results are shown and discussed. Our innovations offer a proper and safe insertion of the prosthesis into the oval window associated with excellent manipulation and handling. At the same time, maximum visualization of the surgical field is achieved, while the stepped-down design of the shaft prevents the prosthesis protruding into the vestibule.     

Combination antiretroviral therapy and recent declines in AIDS incidence and mortality

The reasons for recent declines in AIDS incidence and mortality may include advances in treatment, but these may be confounded by earlier declines in the incidence of human immunodeficiency virus (HIV) infection. To determine whether the declines in AIDS and mortality may, in part, stem from wider use of combination antiretroviral therapy, 622 HIV-positive men with well-characterized dates of seroconversion were followed. In this group, combination therapy came into widespread use in only 1996. In a Cox proportional hazards model, the 1996 calendar period was significantly associated with slower progression to AIDS (relative hazard [RH]=0. 19, 95% confidence interval [CI], 0.05-0.69, P=.01) and death (RH=0. 45, 95% CI, 0.21-0.95, P=.04). Declines in incidence of HIV infection, changes in HIV virulence, and end-point underreporting cannot fully explain the decline in AIDS and death in 1996. The introduction of combination antiretroviral therapy as the standard of care may already have had measurable effects.     

cDNA fingerprinting of osteoprogenitor cells to isolate differentiation stage-specific genes

A cDNA fingerprinting strategy was developed to identify genes based on their differential expression pattern during osteoblast development. Preliminary biological and molecular staging of cDNA pools prepared by global amplification PCR allowed discrim-inating choices to be made in selection of expressed sequence tags (ESTs) to be isolated. Sequencing of selected ESTs confirmed that both known and novel genes can be isolated from any developmental stage of interest, e.g. from primitive progenitors, intermediate precursors or mature osteoblasts. EST expression provides insight into possible interrelated physiological functions and putative interacting molecules during differentiation. This method offers a functional genomics approach to isolate differentiation stage-specific genes in samples as small as a single cell.