1. 
 Lundborg, Magnus, et al.
(författare)

An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations
 2014

Ingår i: Journal of Computational Chemistry.  WileyBlackwell.  01928651. ; 35:3, s. 260269

Tidskriftsartikel (refereegranskat)abstract
 Molecular dynamics simulations is an important application in theoretical chemistry, and with the large highperformance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more costefficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present Trajectory Next Generation (TNG)a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides stateoftheart multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes.


2. 
 Schäfer, Werner, et al.
(författare)

Good urodynamic practices : Uroflowmetry, filling cystometry, and pressureflow studies
 2002

Ingår i: Neurourology and Urodynamics.  07332467. ; 21, s. 261274

Tidskriftsartikel (refereegranskat)abstract
 This is the first report of the International Continence Society (ICS) on the development of comprehensive guidelines for Good Urodynamic Practice for the measurement, quality control, and documentation of urodynamic investigations in both clinical and research environments. This report focuses on the most common urodynamics examinations; uroflowmetry, pressure recording during filling cystometry, and combined pressureflow studies. The basic aspects of good urodynamic practice are discussed and a strategy for urodynamic measurement, equipment setup and configuration, signal testing, plausibility controls, pattern recognition, and artifact correction are proposed. The problems of data analysis are mentioned only when they are relevant in the judgment of data quality. In general, recommendations are made for one specific technique. This does not imply that this technique is the only one possible. Rather, it means that this technique is wellestablished, and gives good results when used with the suggested standards of good urodynamic practice.


3. 
 BillAxelson, Anna, et al.
(författare)

Radical Prostatectomy or Watchful Waiting in Early Prostate Cancer
 2014

Ingår i: New England Journal of Medicine.  Massachusetts Medical Society.  00284793. ; 370:10, s. 932942

Tidskriftsartikel (refereegranskat)abstract
 BackgroundRadical prostatectomy reduces mortality among men with localized prostate cancer; however, important questions regarding longterm benefit remain. MethodsBetween 1989 and 1999, we randomly assigned 695 men with early prostate cancer to watchful waiting or radical prostatectomy and followed them through the end of 2012. The primary end points in the Scandinavian Prostate Cancer Group Study Number 4 (SPCG4) were death from any cause, death from prostate cancer, and the risk of metastases. Secondary end points included the initiation of androgendeprivation therapy. ResultsDuring 23.2 years of followup, 200 of 347 men in the surgery group and 247 of the 348 men in the watchfulwaiting group died. Of the deaths, 63 in the surgery group and 99 in the watchfulwaiting group were due to prostate cancer; the relative risk was 0.56 (95% confidence interval [CI], 0.41 to 0.77; P=0.001), and the absolute difference was 11.0 percentage points (95% CI, 4.5 to 17.5). The number needed to treat to prevent one death was 8. One man died after surgery in the radicalprostatectomy group. Androgendeprivation therapy was used in fewer patients who underwent prostatectomy (a difference of 25.0 percentage points; 95% CI, 17.7 to 32.3). The benefit of surgery with respect to death from prostate cancer was largest in men younger than 65 years of age (relative risk, 0.45) and in those with intermediaterisk prostate cancer (relative risk, 0.38). However, radical prostatectomy was associated with a reduced risk of metastases among older men (relative risk, 0.68; P=0.04). ConclusionsExtended followup confirmed a substantial reduction in mortality after radical prostatectomy; the number needed to treat to prevent one death continued to decrease when the treatment was modified according to age at diagnosis and tumor risk. A large proportion of longterm survivors in the watchfulwaiting group have not required any palliative treatment. (Funded by the Swedish Cancer Society and others.) The randomized Swedish trial of prostatectomy versus watchful waiting in disease detected mainly clinically (not by PSA screening) continues to show a benefit for early prostatectomy. The number of men younger than 65 needed to treat to prevent one death is now four. The Scandinavian Prostate Cancer Group Study Number 4 (SPCG4), a randomized trial of radical prostatectomy versus watchful waiting in men with localized prostate cancer diagnosed before the era of prostatespecific antigen (PSA) testing, showed a survival benefit of radical prostatectomy as compared with observation at 15 years of followup.(1) By contrast, the Prostate Cancer Intervention versus Observation Trial (PIVOT), initiated in the early era of PSA testing, showed that radical prostatectomy did not significantly reduce prostate cancerspecific or overall mortality after 12 years.(2) PSA screening profoundly changes the clinical domain of study. Among other considerations, the substantial additional lead time ...


4. 
 BillAxelson, Anna, et al.
(författare)

Radical prostatectomy versus watchful waiting in localized prostate cancer : the Scandinavian prostate cancer group4 randomized trial
 2008

Ingår i: Journal of the National Cancer Institute.  00278874 . 14602105. ; 100:16, s. 114454

Tidskriftsartikel (refereegranskat)abstract
 BACKGROUND: The benefit of radical prostatectomy in patients with early prostate cancer has been assessed in only one randomized trial. In 2005, we reported that radical prostatectomy improved prostate cancer survival compared with watchful waiting after a median of 8.2 years of followup. We now report results after 3 more years of followup. METHODS: From October 1, 1989, through February 28, 1999, 695 men with clinically localized prostate cancer were randomly assigned to radical prostatectomy (n = 347) or watchful waiting (n = 348). Followup was complete through December 31, 2006, with histopathologic review and blinded evaluation of causes of death. Relative risks (RRs) were estimated using the Cox proportional hazards model. Statistical tests were twosided. RESULTS: During a median of 10.8 years of followup (range = 3 weeks to 17.2 years), 137 men in the surgery group and 156 in the watchful waiting group died (P = .09). For 47 of the 347 men (13.5%) who were randomly assigned to surgery and 68 of the 348 men (19.5%) who were not, death was due to prostate cancer. The difference in cumulative incidence of death due to prostate cancer remained stable after about 10 years of followup. At 12 years, 12.5% of the surgery group and 17.9% of the watchful waiting group had died of prostate cancer (difference = 5.4%, 95% confidence interval [CI] = 0.2 to 11.1%), for a relative risk of 0.65 (95% CI = 0.45 to 0.94; P = .03). The difference in cumulative incidence of distant metastases did not increase beyond 10 years of followup. At 12 years, 19.3% of men in the surgery group and 26% of men in the watchful waiting group had been diagnosed with distant metastases (difference = 6.7%, 95% CI = 0.2 to 13.2%), for a relative risk of 0.65 (95% CI = 0.47 to 0.88; P = .006). Among men who underwent radical prostatectomy, those with extracapsular tumor growth had 14 times the risk of prostate cancer death as those without it (RR = 14.2, 95% CI = 3.3 to 61.8; P < .001). CONCLUSION: Radical prostatectomy reduces prostate cancer mortality and risk of metastases with little or no further increase in benefit 10 or more years after surgery.


5. 


6. 
 Barrera, Tony, et al.
(författare)

Vectorized table driven algorithms for double precision elementary functions using Taylor expansions
 2009

Ingår i: APLIMAT 8th international conference. ; s. 231246

Konferensbidrag (refereegranskat)abstract
 This paper presents fast implementations of the inverse square root and arcsine, both in double precision. In single precision it is often possible to use a small table and one ordinary NewtonRaphson iteration to compute elementary functions such as the square root. In double precision a substantially larger table is necessary to obtain the desired precision, or, if a smaller table is used, the additional NewtonRaphson iterations required to obtain the precision often requires the evaluation of other expensive elementary functions. Furthermore, large tables use a lot of the cash memory that should have been used for the application code.Obtaining the desired precision using a small table can instead be realised by using a higher order method than the second order NewtonRaphson method. A generalization of Newton's method to higher order is Householder's method, which unfortunately often results in very complicated expressions requiring many multiplications, additions, and even divisions.We show how a highorder method can be used, which only requires a few extra additions and multiplications for each degree of higher order. The method starts from the Taylor expansion of the difference of the value of the elementary function and a starting guess value for each iteration. If the Taylor series is truncated after the second term, ordinary Newton iterations are obtained. In several cases it is possible to algebraically simplify the difference between the true value and the starting guess value. In those cases we show that it is advantageous to use the Taylor series to higher order to obtain the fast convergent method. Moreover, we will show how the coefficients of a Chebyshev polynomial can be fitted to give as little error as possible for the functions close to zero and in the same time reduce the terms in the Taylor expansion.In the paper we benchmark two example implementations of the method on the x86_64 architecture. The first is the inverse square root, where the actual table (to 12 bit precision) is provided by the processor hardware. The inverse square root is important in many application programs, including computer graphics, and explicit particle simulation codes, for instance the Monte Carlo and Molecular Dynamics methods of statistical mechanics. The other example is the arcsine function, which has a slow converging Taylor expansion and where no tables are provided by the hardware. The vectorized versions of the implementations of the inverse square root are 3.5 times faster than compiled code on the Athlon64 and about 5 times faster on the Core 2. The scalar version of the arcsine function is, depending on order and table size, between 2 and 3 times faster than the compiled code, and the vectorized version is between 3 and 4 times faster on the Athlon64, while it is between 4 and 5 times faster than the compiled version on the Core 2.


7. 
 Barrera, Tony, et al.
(författare)

Vectorized table driven algorithms for double precision elementary functions using taylor expansions
 2009

Ingår i: Aplimat: journal of applied mathematics.  13376365. ; 2:3, s. 171187

Tidskriftsartikel (refereegranskat)abstract
 This paper presents fast implementations of the inverse square root and arcsine, both in double precision. In single precision it is often possible to use a small table and one ordinary NewtonRaphson iteration to compute elementary functions such as the square root. In double precision a substantially larger table is necessary to obtain the desired precision, or, if a smaller table is used, the additional NewtonRaphson iterations required to obtain the precision often requires the evaluation of other expensive elementary functions. Furthermore, large tables use a lot of the cash memory that should have been used for the application code. Obtaining the desired precision using a small table can instead be realised by using a higher order method than the second order NewtonRaphson method. A generalization of Newton's method to higher order is Householder's method, which unfortunately often results in very complicated expressions requiring many multiplications, additions, and even divisions. We show how a highorder method can be used, which only requires a few extra additions and multiplications for each degree of higher order. The method starts from the Taylor expansion of the difference of the value of the elementary function and a starting guess value for each iteration. If the Taylor series is truncated after the second term, ordinary Newton iterations are obtained. In several cases it is possible to algebraically simplify the difference between the true value and the starting guess value. In those cases we show that it is advantageous to use the Taylor series to higher order to obtain the fast convergent method. Moreover, we will show how the coefficients of a Chebyshev polynomial can be fitted to give as little error as possible for the functions close to zero and in the same time reduce the terms in the Taylor expansion. In the paper we benchmark two example implementations of the method on the x86_64 architecture. The first is the inverse square root, where the actual table (to 12 bit precision) is provided by the processor hardware. The inverse square root is important in many application programs, including computer graphics, and explicit particle simulation codes, for instance the Monte Carlo and Molecular Dynamics methods of statistical mechanics. The other example is the arcsine function, which has a slow converging Taylor expansion and where no tables are provided by the hardware. The vectorized versions of the implementations of the inverse square root are 3.5 times faster than compiled code on the Athlon64 and about 5 times faster on the Core 2. The scalar version of the arcsine function is, depending on order and table size, between 2 and 3 times faster than the compiled code, and the vectorized version is between 3 and 4 times faster on the Athlon64, while it is between 4 and 5 times faster than the compiled version on the Core 2.


8. 
 BillAxelson, Anna, et al.
(författare)

Radical Prostatectomy versus Watchful Waiting in Early Prostate Cancer
 2011

Ingår i: New England Journal of Medicine.  00284793 . 15334406. ; 364:18, s. 17081717

Tidskriftsartikel (refereegranskat)abstract
 BACKGROUNDIn 2008, we reported that radical prostatectomy, as compared with watchful waiting, reduces the rate of death from prostate cancer. After an additional 3 years of followup, we now report estimated 15year results.METHODSFrom October 1989 through February 1999, we randomly assigned 695 men with early prostate cancer to watchful waiting or radical prostatectomy. Followup was complete through December 2009, with histopathological review of biopsy and radicalprostatectomy specimens and blinded evaluation of causes of death. Relative risks, with 95% confidence intervals, were estimated with the use of a Cox proportionalhazards model.RESULTSDuring a median of 12.8 years, 166 of the 347 men in the radicalprostatectomy group and 201 of the 348 in the watchfulwaiting group died (P=0.007). In the case of 55 men assigned to surgery and 81 men assigned to watchful waiting, death was due to prostate cancer. This yielded a cumulative incidence of death from prostate cancer at 15 years of 14.6% and 20.7%, respectively (a difference of 6.1 percentage points; 95% confidence interval [CI], 0.2 to 12.0), and a relative risk with surgery of 0.62 (95% CI, 0.44 to 0.87; P=0.01). The survival benefit was similar before and after 9 years of followup, was observed also among men with lowrisk prostate cancer, and was confined to men younger than 65 years of age. The number needed to treat to avert one death was 15 overall and 7 for men younger than 65 years of age. Among men who underwent radical prostatectomy, those with extracapsular tumor growth had a risk of death from prostate cancer that was 7 times that of men without extracapsular tumor growth (relative risk, 6.9; 95% CI, 2.6 to 18.4).CONCLUSIONSRadical prostatectomy was associated with a reduction in the rate of death from prostate cancer. Men with extracapsular tumor growth may benefit from adjuvant local or systemic treatment.


9. 
 BillAxelson, Anna, et al.
(författare)

Radical prostatectomy versus watchful waiting in early prostate cancer
 2005

Ingår i: New England Journal of Medicine.  00284793. ; 352:19, s. 19771984

Tidskriftsartikel (refereegranskat)abstract
 BACKGROUND: In 2002, we reported the initial results of a trial comparing radical prostatectomy with watchful waiting in the management of early prostate cancer. After three more years of followup, we report estimated 10year results. METHODS: From October 1989 through February 1999, 695 men with early prostate cancer (mean age, 64.7 years) were randomly assigned to radical prostatectomy (347 men) or watchful waiting (348 men). The followup was complete through 2003, with blinded evaluation of the causes of death. The primary end point was death due to prostate cancer, the secondary end points were death from any cause, metastasis, and local progression. RESULTS: During a median of 8.2 years of followup, 83 men in the surgery group and 106 men in the watchfulwaiting group died (P=0.04). In 30 of the 347 men assigned to surgery (8.6 percent) and 50 of the 348 men assigned to watchful waiting (14.4 percent), death was due to prostate cancer. The difference in the cumulative incidence of death due to prostate cancer increased from 2.0 percentage points after 5 years to 5.3 percentage points after 10 years, for a relative risk of 0.56 (95 percent confidence interval, 0.36 to 0.88, P=0.01 by Gray's test). For distant metastasis, the corresponding increase was from 1.7 to 10.2 percentage points, for a relative risk in the surgery group of 0.60 (95 percent confidence interval, 0.42 to 0.86, P=0.004 by Gray's test), and for local progression, the increase was from 19.1 to 25.1 percentage points, for a relative risk of 0.33 (95 percent confidence interval, 0.25 to 0.44, P<0.001 by Gray's test). CONCLUSIONS: Radical prostatectomy reduces diseasespecific mortality, overall mortality, and the risks of metastasis and local progression. The absolute reduction in the risk of death after 10 years is small, but the reductions in the risks of metastasis and local tumor progression are substantial. Copyright © 2005 Massachusetts Medical Society.


10. 
 BillAxelson, Anna, et al.
(författare)

Radical prostatectomy versus watchful waiting in early prostate cancer.
 2011

Ingår i: The New England journal of medicine.  15334406. ; 364:18, s. 170817

Forskningsöversikt (refereegranskat)abstract
 In 2008, we reported that radical prostatectomy, as compared with watchful waiting, reduces the rate of death from prostate cancer. After an additional 3 years of followup, we now report estimated 15year results.

