Computational chemistry on Fujitsu vector-parallel processors: Development and performance of applications software

In this and a preceding paper, we provide an introduction to the Fujitsu VPP range of vector-parallel supercomputers and to some of the computational chemistry software available for the VPP. Here, we consider the implementation and performance of seven popular chemistry application packages. The codes discussed range from classical molecular dynamics to semiempirical and ab initio quantum chemistry. All have evolved from sequential codes, and have typically been parallelised using a replicated data approach. As such they are well suited to the large-memory/fast-processor architecture of the VPP. For one code, CASTEP, a distributed-memory data-driven parallelisation scheme is presented. (C) 2000 Published by Elsevier Science B.V. All rights reserved.

L-studio/cpfg: A software system for modeling plants

L-studio/cpfg is a plant modeling software system designed for Windows 95/98/NT platforms. Its key components are the L-system-based plant simulator cpfg and the modeling environment called L-studio. We overview version 1.0 of this system from the user's perspective.

Smart Alerts: Development of Software to Optimize Data Monitoring

Dherte PM, Negrao MPG, Mori Neto S, Holzhacker R, Shimada V, Taberner P, Carmona MJC - Smart Alerts: Development of a Software to Optimize Data Monitoring. Background and objectives: Monitoring is useful for vital follow-ups and prevention, diagnosis, and treatment of several events in anesthesia. Although alarms can be useful in monitoring they can cause dangerous user`s desensitization. The objective of this study was to describe the development of specific software to integrate intraoperative monitoring parameters generating ""smart alerts"" that can help decision making, besides indicating possible diagnosis and treatment. Methods: A system that allowed flexibility in the definition of alerts, combining individual alarms of the parameters monitored to generate a more elaborated alert system was designed. After investigating a set of smart alerts, considered relevant in the surgical environment, a prototype was designed and evaluated, and additional suggestions were implemented in the final product. To verify the occurrence of smart alerts, the system underwent testing with data previously obtained during intraoperative monitoring of 64 patients. The system allows continuous analysis of monitored parameters, verifying the occurrence of smart alerts defined in the user interface. Results: With this system a potential 92% reduction in alarms was observed. We observed that in most situations that did not generate alerts individual alarms did not represent risk to the patient. Conclusions: Implementation of software can allow integration of the data monitored and generate information, such as possible diagnosis or interventions. An expressive potential reduction in the amount of alarms during surgery was observed. Information displayed by the system can be oftentimes more useful than analysis of isolated parameters.

The rms1 mutant of pea has elevated indole-3-acetic acid levels and reduced root-sap zeatin riboside content but increased branching controlled by graft-transmissible signal(s)

Rms1 is one of the series of five ramosus loci in pea (Pisum sativum L.) in which recessive mutant alleles confer increased branching at basal and aerial vegetative nodes. Shoots of the nonallelic rms1 and rms2 mutants are phenotypically similar in most respects. However, we found an up to 40-fold difference in root-sap zeatin riboside ([9R]Z) concentration between rms1 and rms2 plants. Compared with wild-type (WT) plants, the concentration of [9R]Z in rms1 root sap was very low and the concentration in rms2 root sap was slightly elevated. To our knowledge, the rms1 mutant is therefore the second ramosus mutant (rms4 being the first) to be characterized with low root-sap [9R]Z content. Like rms2, the apical bud and upper nodes of rms1 plants contain elevated indole-3-acetic acid levels compared with WT shoots. Therefore, the rms1 mutant demonstrates that high shoot auxin levels and low root-sap cytokinin levels are not necessarily correlated with increased apical dominance in pea. A graft-transmissible basis of action has been demonstrated for both mutants from reciprocal grafts between mutant and WT plants. Branching was also largely inhibited in rms1 shoots when grafted to rms2 rootstocks, but was not inhibited in rms2 shoots grafted to rms1 rootstocks. These grafting results are discussed, along with the conclusion that hormone-like signals other than auxin and cytokinin are also involved.

The generation of H-1-NMR-detectable mobile lipid in stimulated lymphocytes: Relationship ts cellular activation, the cell cycle, and phosphatidylcholine-specific phospholipase C

Mobile Lipids detected using H-1-NMR in stimulated lymphocytes were correlated with cell cycle phase, expression of the interleukin-2 receptor alpha and proliferation to assess the activation status of the lymphocytes. Mobile lipid levels, IL-2R alpha expression and proliferation increased after treatment with PMA and ionomycin. PMA or ionomycin stimulation alone induced increased IL-2R alpha expressiom but not proliferation, PMA- but not ionomycin-stimulation generated mobile lipid, Treatment with anti-CD3 antibody did not increase IL-2R alpha expression or proliferation but did generate increased amounts of mobile lipid, The cell cycle status of thymocytes treated with anti-CD3, PMA or ionomycin alone indicated an. accumulation of the cells in the G(1) phase of the cell cycle, The generation of mobile lipid was abrogated in anti-CD3 antibody-stimulated thymic lymphocytes but not in splenic lymphocytes, using a phosphatidylcholine-specific phospholipase C (PC-PLC) inhibitor which blocked cells in the G(1)/S phase of the cell cycle, This suggests that the H-1-NMR-detectable mobile Lipid may be generated in anti-CD3 antibody-stimulated thymic lymphocytes by the action of PC-PLC activity via the catabolism of PC, in the absence of classical signs of activation. (C) 1997 Academic Press.

Impact of Atypical Retardation Patterns on Detection of Glaucoma Progression using the GDx with Variable Corneal Compensation

PURPOSE: To evaluate the impact of atypical retardation patterns (ARP) on detection of progressive retinal nerve fiber layer (RNFL) loss using scanning laser polarimetry with variable corneal compensation (VCC). DESIGN: Observational cohort study. METHODS: The study included 377 eyes of 221 patients with a median follow-up of 4.0 years. Images were obtained annually with the GDx VCC (Carl Zeiss Med, itec Inc, Dublin, California, USA), along with optic disc stereophotographs and standard automated perimetry (SAP) visual fields. Progression was determined by the Guided Progression Analysis software for SAP and by masked assessment of stereophotographs by expert graders. The typical scan score (TSS) was used to quantify the presence of ARPs on GDx VCC images. Random coefficients models were used to evaluate the relationship between ARP and RNFL thickness measurements over time. RESULTS: Thirty-eight eyes (10%) showed progression over time on visual fields, stereophotographs, or both. Changes in TSS scores from baseline were significantly associated with changes in RNFL thickness measurements in both progressing and nonprogressing eyes. Each I unit increase in TSS score was associated with a 0.19-mu m decrease in RNFL thickness measurement (P < .001) over time. CONCLUSIONS: ARPs had a significant effect on detection of progressive RNFL loss with the GDx VCC. Eyes with large amounts of atypical patterns, great fluctuations on these patterns over time, or both may show changes in measurements that can appear falsely as glaucomatous progression or can mask true changes in the RNFL. (Am J Ophthalmol 2009;148:155-163. (C) 2009 by Elsevier Inc. All rights reserved.)

Can Mobile Units Improve the Strategies for Cervical Cancer Prevention?

Cervical cancer is a serious public health problem in women in developing countries because of absence or ineffectiveness of screening programs. Several biases to access medical care and inequity of public health system in a continental country like Brazil limit the implementation of adequate programs to appropriately prevent the cervical cancer. Therefore, the aim of this study was to evaluate the results of applying the mobile unit (MU) for cervical cancer screening. From May 2003 to May 2004, a cervical cancer screening was offered to women aged 20-69 years, residing in 19 municipal districts of the Barretos county region, in Sao Paulo. Out of the 9,560 examination available, 2,964 (31%) women underwent screening. The medium distance traveled by the MU was 45 km. The medium time spent by women in the MU for completion of the questionnaire and doing the exam was 20 minutes. It was observed that 17.0% of women screened had never had the test or had not had it repeated within the last 3 years. The negative response was more common among women aged 20 to 29 years and 60 to 69 years and among women with less schooling and lower socio-economic income (P < 0.05). MU can significantly overcome the chronic deficiency of public health system accessibility offering opportunity to these women to participate in screening programs. Diagn. Cytopathol. 2010;38:727-730. (C) 2009 Wiley-Liss, Inc.

Program for Prostate Cancer Screening Using a Mobile Unit: Results From Brazil

OBJECTIVES To evaluate the initial results of a prostate cancer screening program using mobile units in Brazil. METHODS Since 2004, we have conducted a program of prostate cancer screening using mobile units across 231 municipalities from 6 Brazilian states. RESULTS A total of 17 571 men were evaluated by clinical history, digital rectal examination (DRE), and serum free and total prostate-specific antigen (PSA) levels. The recommendations for biopsy were a PSA level of >= 4.0 ng/mL, DRE findings suspicious for cancer, or a PSA level of 2.5-4.0 ng/mL with a percent-free PSA level <15%. The biopsy protocol included 12 biopsy cores from the peripheral zone, 2 from the transition zone, and additional sampling of suspicious areas. The cumulative cancer detection rate was 3.7%. The main indication for biopsy was a PSA level of >= 4.0 ng/mL (51.2%), with a positive predictive value (PPV) of 44.1%. Another 19.7% of biopsied men had suspicious DRE findings with a normal PSA level (PPV 23.5%). A percent-free PSA level of <15% in men with a PSA level of 2.5-4.0 ng/mL and normal DRE findings yielded a PPV of 31.1%. The PPV was greater (70.9%) for the 7.1% of men with both suspicious DRE findings and a PSA level of >4.0 ng/mL. Most cancers were Stage T1-T2 (93.4%), and the percentage of Gleason score of >= 7 was 32.5%. The proportion of insignificant cancers according to Epstein`s criteria was 13.5%. CONCLUSIONS A mobile prostate cancer screening unit enabled an underserved population to gain access to specialized care through the public healthcare system. The cancer detection rate in this population was similar to those from international studies. UROLOGY 76: 1052-1057, 2010. (C) 2010 Published by Elsevier Inc.

A Comparison of Rates of Change in Neuroretinal Rim Area and Retinal Nerve Fiber Layer Thickness in Progressive Glaucoma

PURPOSE. To evaluate and compare rates of change in neuro-retinal rim area (RA) and retinal nerve fiber layer thickness (RNFLT) measurements in glaucoma patients, those with suspected glaucoma, and normal subjects observed over time. METHODS. In this observational cohort study, patients recruited from two longitudinal studies (Diagnostic Innovations in Glaucoma Study-DIGS and African Descent and Evaluation Study-ADAGES) were observed with standard achromatic perimetry (SAP), optic disc stereophotographs, confocal scanning laser ophthalmoscopy (HRT-3; Heidelberg Engineering, Heidelberg, Germany), and scanning laser polarimetry (GDx-VCC; Carl Zeiss Meditec, Inc., Dublin, CA). Glaucoma progression was determined by the Guided Progression Analysis software for standard automated perimetry [SAP] and by masked assessment of serial optic disc stereophotographs by expert graders. Random-coefficients models were used to evaluate rates of change in average RNFLT and global RA measurements and their relationship with glaucoma progression. RESULTS. At baseline, 194 (31%) eyes were glaucomatous, 347 (55%) had suspected glaucoma, and 88 (14%) were normal. Forty-six (9%) eyes showed progression by SAP and/or stereophotographs, during an average follow-up of 3.3 (+/-0.7) years. The average rate of decline for RNFLT measurements was significantly higher in the progressing group than in the non-progressing group (-0.65 vs. -0.11 mu m/y, respectively; P < 0.001), whereas RA decline was not significantly different between these groups (-0.0058 vs. -0.0073 mm(2)/y, respectively; P = 0.727). The areas under the receiver operating characteristic (ROC) curves used to discriminate progressing versus nonprogressing eyes were 0.811 and 0.507 for the rates of change in the RNFLT and RA, respectively (P < 0.001). CONCLUSIONS. The ability to discriminate eyes with progressing glaucoma by SAP and/or stereophotographs from stable eyes was significantly greater for RNFLT than for RA measurements. (Invest Ophthalmol Vis Sci. 2010;51:3531-3539) DOI: 10.1167/iovs.09-4350

Agreement for Detecting Glaucoma Progression with the GDx Guided Progression Analysis, Automated Perimetry, and Optic Disc Photography

Purpose: To evaluate the ability of the GDx Variable Corneal Compensation (VCC) Guided Progression Analysis (GPA) software for detecting glaucomatous progression. Design: Observational cohort study. Participants: The study included 453 eyes from 252 individuals followed for an average of 46 +/- 14 months as part of the Diagnostic Innovations in Glaucoma Study. At baseline, 29% of the eyes were classified as glaucomatous, 67% of the eyes were classified as suspects, and 5% of the eyes were classified as healthy. Methods: Images were obtained annually with the GDx VCC and analyzed for progression using the Fast Mode of the GDx GPA software. Progression using conventional methods was determined by the GPA software for standard automated achromatic perimetry (SAP) and by masked assessment of optic disc stereophotographs by expert graders. Main Outcome Measures: Sensitivity, specificity, and likelihood ratios (LRs) for detection of glaucoma progression using the GDx GPA were calculated with SAP and optic disc stereophotographs used as reference standards. Agreement among the different methods was reported using the AC(1) coefficient. Results: Thirty-four of the 431 glaucoma and glaucoma suspect eyes (8%) showed progression by SAP or optic disc stereophotographs. The GDx GPA detected 17 of these eyes for a sensitivity of 50%. Fourteen eyes showed progression only by the GDx GPA with a specificity of 96%. Positive and negative LRs were 12.5 and 0.5, respectively. None of the healthy eyes showed progression by the GDx GPA, with a specificity of 100% in this group. Inter-method agreement (AC1 coefficient and 95% confidence intervals) for non-progressing and progressing eyes was 0.96 (0.94-0.97) and 0.44 (0.28-0.61), respectively. Conclusions: The GDx GPA detected glaucoma progression in a significant number of cases showing progression by conventional methods, with high specificity and high positive LRs. Estimates of the accuracy for detecting progression suggest that the GDx GPA could be used to complement clinical evaluation in the detection of longitudinal change in glaucoma. Financial Disclosure(s): Proprietary or commercial disclosure may be found after the references. Ophthalmology 2010; 117: 462-470 (C) 2010 by the American Academy of Ophthalmology.