The expanding small heat-shock protein family, and structure predictions of the conserved "alpha-crystallin domain"

The ever-increasing number of proteins identified as belonging to the family of small heat-shock proteins (shsps) and alpha-crystallins enables us to reassess the phylogeny of this ubiquitous protein family. While the prokaryotic and fungal representatives are not properly resolved, most of the plant and animal shsps and related proteins are clearly grouped in distinct clades, reflecting a history of repeated gene duplications. The members of the shsp family are characterized by the presence of a conserved homologous "alpha-crystallin domain," which sometimes is present in duplicate. Predictions are made of secondary structure and solvent accessibility of this domain, which together with hydropathy profiles and intron positions support the presence of two similar hydrophobic beta-sheet-rich motifs, connected by a hydrophilic alpha-helical region. Together with an overview of the newly characterized members of the shsp family, these data help to define this family as being involved as stable structural proteins and as molecular chaperones during normal development and induced under pathological and stressful conditions.     

DNA-Directed alkylating agents. 7. Synthesis, DNA interaction, and antitumor activity of bis(hydroxymethyl)- and bis(carbamate)-substituted pyrrolizines and imidazoles

A series of bis(hydroxymethyl)-substituted imidazoles, thioimidazoles, and pyrrolizines and related bis(carbamates), linked to either 9-anilinoacridine (intercalating) or 4-(4-quinolinylamino)benzamide (minor groove binding) carriers, were synthesized and evaluated for sequence-specific DNA alkylation and cytotoxicity. The imidazole and thioimidazole analogues were prepared by initial synthesis of [(4-aminophenyl)alkyl]imidazole-, thioimidazole-, or pyrrolizine dicarboxylates, coupling of these with the desired carrier, and reduction to give the required bis(hydroxymethyl) alkylating moiety. The pyrrolizines were the most reactive alkylators, followed by the thioimidazoles, while the imidazoles were unreactive. The pyrrolizines and some of the thioimidazoles cross-linked DNA, as measured by agarose gel electrophoresis. Strand cleavage assays showed that none of the compounds reacted at purine N7 or N3 sites in the gpt region of the plasmid gpt2Eco, but the polymerase stop assay showed patterns of G-alkylation in C-rich regions. The corresponding thioimidazole bis(carbamates) were more selective than the bis(hydroxymethyl) pyrrolizines, with high-intensity bands at 5'-NCCN, 5'-NGCN and 5'-NCGN sequences in the PCR stopping assay ( indicates block sites). The data suggest that these targeted compounds, like the known thioimidazole bis(carbamate) carmethizole, alkylate exclusively at guanine residues via the 2-amino group, with little or no alkylation at N3 and N7 guanine or adenine sites. The cytotoxicities of the compounds correlated broadly with their reactivities, with the bis(hydroxymethyl)imidazoles being the least cytotoxic (IC50s >1 microM; P388 leukemia) and with the intercalator-linked analogues being more cytotoxic than the corresponding minor-groove-targeted ones. This was true also for the more reactive thioimidazole bis(carbamates) (IC50s 0.8 and 11 microM, respectively), but both were more active than the analogous "untargeted" carmethizole (IC50 20 microM). The bis(hydroxymethyl)pyrrolizine analogues were the most cytotoxic, with IC50s as low as 0.03 microM.     

'98 Escherichia coli SWISS-2DPAGE database update

The combination of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), computer image analysis and several protein identification techniques allowed the Escherichia coli SWISS-2DPAGE database to be established. This is part of the ExPASy molecular biology server accessible through the WWW at the URL address http://www.expasy.ch/ch2d/ch2d-top.html . Here we report recent progress in the development of the E. coli SWISS-2DPAGE database. Proteins were separated with immobilized pH gradients in the first dimension and sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. To increase the resolution of the separation and thus the number of identified proteins, a variety of wide and narrow range immobilized pH gradients were used in the first dimension. Micropreparative gels were electroblotted onto polyvinylidene difluoride membranes and spots were visualized by amido black staining. Protein identification techniques such as amino acid composition analysis, gel comparison and microsequencing were used, as well as a recently described Edman "sequence tag" approach. Some of the above identification techniques were coupled with database searching tools. Currently 231 polypeptides are identified on the E. coli SWISS-2DPAGE map: 64 have been identified by N-terminal microsequencing, 39 by amino acid composition, and 82 by sequence tag. Of 153 proteins putatively identified by gel comparison, 65 have been confirmed. Many proteins have been identified using more than one technique. Faster progress in the E. coli proteome project will now be possible with advances in biochemical methodology and with the completion of the entire E. coli genome.     

Comparison of the frequency and enjoyability of pleasant events in cocaine abusers vs. non-abusers using a standardized behavioral inventory

AIMS: To examine whether cocaine abusers differ from non-abusers in their frequency and enjoyability of engaging in various "pleasant events", in order to approximate the density of positive reinforcement experienced in their natural environment. DESIGN: Comparisons of cocaine abusers to normative data and matched controls. SETTING: An outpatient substance abuse treatment center in Burlington, Vermont, USA. PARTICIPANTS: Subjects included 100 individuals enrolled in outpatient treatment for cocaine abuse or dependence and 50 community volunteers without histories of drug abuse or other major psychiatric illness and matched to cocaine-dependent patients on age, sex and SES. MEASUREMENTS: Diagnostic assessments were based upon clinical interviews using the DSM-III-R checklist. The primary focus of this study was the Pleasant Events Schedule (PES), a self-rated behavioral inventory of the frequency and enjoyability of engaging in "pleasant" activities. Cocaine use history, treatment outcome and other relevant variables were also assessed. FINDINGS: Cocaine abusers reliably reported lower frequency of non-social, introverted, passive outdoor and mood-related activities than controls. These differences remained after controlling for demographic and life-style differences between groups, with the exception of mood-related activities. Perceived enjoyability of the activities did not differ across groups. Intravenous cocaine use and prior treatment for cocaine abuse predicted particularly low frequency of pleasant activities. Greater frequency of non-social activities predicted better treatment outcome. CONCLUSIONS: Drug abuse is associated with low density of certain types of non-drug reinforcement. Systematic increases in these activities may improve treatment outcome.     

Operative management of Haglund's deformity in the nonathlete: a retrospective study

Haglund's deformity, or "pump bump," is a common cause of posterior heel pain. Management of the condition usually consists of nonoperative therapy. This study presents a retrospective study of 65 cases (53 patients), with symptomatic Haglund's deformity in nonathletes (13 male and 40 female), who presented during a 4-year period (1989-1994). Sixty-five percent (39 heels) of these patients failed to respond to nonoperative therapy for an average of 62 weeks, (range, 4-260 weeks). This group of patients went on to operative treatment. Surgical management consisted of excision of the posterior calcaneal tuberosity through a medial longitudinal incision with debridement, reattachment of the Achilles tendon using bone anchors, and 4 weeks of postoperative immobilization. Thirty-nine patients (74%) were contacted for follow-up. The average follow-up period for these patients was 155 weeks, (range, 92-335 weeks). There were 50% excellent results, 47% good results, 3% fair results (1 patient), and no poor results. The Maryland Foot Score for operated heels was an average of 67/100 preoperative and an average of 92/100 postoperative. On unoperated heels the score was an average of 81/100 at first evaluation and an average of 86/100 at final evaluation. Complications included one recurrence of painful prominence, one wound infection, and one incisional neuroma. The outcome of these cases demonstrated that in those patients who fail nonoperative treatment, surgical treatment of Haglund's deformity produces a predictably good surgical result when performed using the technique described.     

Eucapnic voluntary hyperventilation as a bronchoprovocation technique: development of a standarized dosing schedule in asthmatics

A variety of dosing schedules have been reported for the hyperventilation method of broncho-provocation testing. To evaluate the effect of challenge technique on the bronchoconstrictive response, we had 16 subjects perform eucapnic voluntary hyperventilation (EVH) with dry, room temperature gas using four different dosing schedules. The hyperventilation challenge dosages included the following: (1) a target minute ventilation (VE) of 20 x FEV1 for 6 min; (2) a target VE of 15 x FEV1 for 12 min; (3) an interrupted challenge with a target VE of 30 x FEV1 for 2 min repeated 3 times; and (4) a target VE of 30 x FEV1 for 6 min. Challenges 2, 3, and 4 gave identical absolute ventilatory challenges (identical factor FEV1 x minutes) but at different VE dosages or time. Challenges 1 and 4 were of identical length, but different target VE. The mean postchallenge fall in FEV1 was 16.6 +/- 10.9%, 11.0 +/- 8.1%, 19.6 +/- 9.9%, and 26.7 +/- 11.3% for challenges 1, 2, 3, and 4, respectively. The response to an identical EVH challenge (FEV1 x 30 for 6 min) was reproducible when performed on separate days. We conclude that the challenge technique used for hyperventilation testing will have a significant impact on the bronchoconstrictive response and must be taken into account when interpreting study results. Tests may be quantitatively comparable over a narrow range of challenge time and VE. We recommend that a 6-min uninterrupted EVH challenge using dry, room temperature gas at a target VE of 30 x FEV1 be adopted as the "standard" challenge.     

Making DRAM refresh predictable

Embedded control systems with hard real-time constraints require that deadlines are met at all times or the system may malfunction with potentially catastrophic consequences. Schedulability theory can assure deadlines for a given task set when periods and worst-case execution times (WCETs) of tasks are known. While periods are generally derived from the problem specification, a task??s code needs to be statically analyzed to derive safe and tight bounds on its WCET. Such static timing analysis abstracts from program input and considers loop bounds and architectural features, such as pipelining and caching. However, unpredictability due to dynamic memory (DRAM) refresh cannot be accounted for by such analysis, which limits its applicability to systems with static memory (SRAM). In this paper, we assess the impact of DRAM refresh on task execution times and demonstrate how predictability is adversely affected leading to unsafe hard real-time system design. We subsequently contribute a novel and effective approach to overcome this problem through software-initiated DRAM refresh. We develop (1)?a?pure software and (2)?a?hybrid hardware/software refresh scheme. Both schemes provide predictable timings and fully replace the classical hardware auto-refresh. We discuss implementation details based on this design for multiple concrete embedded platforms and experimentally assess the benefits of different schemes on these platforms. We further formalize the integration of variable latency memory references into a data-flow framework suitable for static timing analysis to bound a task??s memory latencies with regard to their WCET. The resulting predictable execution behavior in the presence of DRAM refresh combined with the additional benefit of reduced access delays is unprecedented, to the best of our knowledge.     

Realizing quality improvement through test driven development: results and experiences of four industrial teams

Test-driven development (TDD) is a software development practice that has been used sporadically for decades. With this practice, a software engineer cycles minute-by-minute between writing failing unit tests and writing implementation code to pass those tests. Test-driven development has recently re-emerged as a critical enabling practice of agile software development methodologies. However, little empirical evidence supports or refutes the utility of this practice in an industrial context. Case studies were conducted with three development teams at Microsoft and one at IBM that have adopted TDD. The results of the case studies indicate that the pre-release defect density of the four products decreased between 40% and 90% relative to similar projects that did not use the TDD practice. Subjectively, the teams experienced a 15–35% increase in initial development time after adopting TDD.