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1. Distinct spin and orbital dynamics in Sr2RuO4

Author

Suzuki, H., Wang, L., Bertinshaw, J., Strand, H. U. R., Käser, S., Krautloher, M., Yang, Z., Wentzell, N., Parcollet, O., Jerzembeck, F., Kikugawa, N., Mackenzie, A. P., Georges, A., Hansmann, P., Gretarsson, H., and Keimer, B.

Published
2023
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2. Single particle tracking uncertainties in ion imaging

Author

Burker, A., Bergauer, T., Hirtl, A., Irmler, C., Kaser, S., Knäusl, B., Pitters, F., and Ulrich-Pur, F.

Subjects
Physics - Medical Physics, Physics - Instrumentation and Detectors
Abstract

An extensive comparison of the path uncertainty in single particle tracking systems for ion imaging was carried out based on Monte Carlo simulations. The spatial resolution as function of system parameters such as geometry, detector properties and the energy of proton and helium beams was investigated to serve as a guideline for hardware developments. Primary particle paths were sampled within a water volume and compared to the most likely path estimate obtained from detector measurements, yielding a depth-dependent uncertainty envelope. The maximum uncertainty along this curve was converted to a conservative estimate of the minimal radiographic pixel spacing for a single set of parameter values. Simulations with various parameter settings were analysed to obtain an overview of the reachable pixel spacing as function of system parameters. The results were used to determine intervals of detector material budget and position resolution that yield a pixel spacing small enough for clinical dose calculation. To ensure a pixel spacing below 2 mm, the material budget of a detector should remain below 0.25 % for a position resolution of 200 $\mathrm{\mu m}$ or below 0.75 % for a resolution of 10 $\mathrm{\mu m}$. Using protons, a sub-millimetre pixel size could not be achieved for a phantom size of 300 mm or at a large clearance. With helium ions, a sub-millimetre pixel spacing could be achieved even for a large phantom size and clearance, provided the position resolution was less than 100 $\mathrm{\mu m}$ and material budget was below 0.75 %., Comment: 19 pages, 6 figures, submitted to Phys. Med. Biol

Published
2020

3. Imaging with protons at MedAustron

Author

Ulrich-Pur, F., Bergauer, T., Burker, A., Hatamikia, S., Hirtl, A., Irmler, C., Kaser, S., Paulitsch, P., Pitters, F., and Teufelhart, V.

Subjects
Physics - Instrumentation and Detectors, Physics - Medical Physics
Abstract

Ion beam therapy has become a frequently applied form of cancer therapy over the last years. The advantage of ion beam therapy over conventional radiotherapy using photons is the strongly localized dose deposition, leading to a reduction of dose applied to surrounding healthy tissue. Currently, treatment planning for proton therapy is based on X-ray computed tomography, which entails certain sources of inaccuracy in alculation of the stopping power (SP). A more precise method to acquire the SP is to directly use high energy protons (or other ions such as carbon) and perform proton computed tomography (pCT). With this method, the ions are tracked prior to entering and after leaving the patient and finally their residual energy is measured at the very end. Therefore, an ion imaging demonstrator, comprising a tracking telescope made from double-sided silicon strip detectors and a range telescope as a residual energy detector, was set up. First measurements with this setup were performed at beam tests at MedAustron, a center for ion therapy and research in \mbox{Wiener Neustadt}, \mbox{Austria}. The facility provides three rooms for cancer treatment with proton beams as well as one which is dedicated to non-clinical research. This contribution describes the principle of ion imaging with proton beams in general as well as the design of the experimental setup. Moreover, first results from simulations and recent beam tests as well as ideas for future developments will be presented., Comment: 7 pages, 11 figures, proceedings of the "HSTD12: 12th International "Hiroshima" Symposium on the Development and Application of Semiconductor Tracking Detectors (HSTD12)", 14-18 Dec 2019, Hiroshima (Japan), to be submitted to Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment

Published
2020
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6. Distinct spin and orbital dynamics in Sr2RuO4.

Author

Suzuki, H., Wang, L., Bertinshaw, J., Strand, H. U. R., Käser, S., Krautloher, M., Yang, Z., Wentzell, N., Parcollet, O., Jerzembeck, F., Kikugawa, N., Mackenzie, A. P., Georges, A., Hansmann, P., Gretarsson, H., and Keimer, B.

Subjects
SPIN excitations, X-ray scattering, INELASTIC scattering, ELECTRONIC excitation, COOPER pair, ELECTRON configuration
Abstract

The unconventional superconductor Sr2RuO4 has long served as a benchmark for theories of correlated-electron materials. The determination of the superconducting pairing mechanism requires detailed experimental information on collective bosonic excitations as potential mediators of Cooper pairing. We have used Ru L3-edge resonant inelastic x-ray scattering to obtain comprehensive maps of the electronic excitations of Sr2RuO4 over the entire Brillouin zone. We observe multiple branches of dispersive spin and orbital excitations associated with distinctly different energy scales. The spin and orbital dynamical response functions calculated within the dynamical mean-field theory are in excellent agreement with the experimental data. Our results highlight the Hund metal nature of Sr2RuO4 and provide key information for the understanding of its unconventional superconductivity. The authors present resonant inelastic x-ray scattering measurements of Sr2RuO4 in the normal Fermi-liquid state. They find that spin excitations are confined below 200 meV, while orbital fluctuations appear only at higher energies. This separation of energy scales is a hallmark of Hund's-rule-induced electron correlations. [ABSTRACT FROM AUTHOR]

Published
2023
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7. Normal width of the linea alba, prevalence, and risk factors for diastasis recti abdominis in adults, a cross-sectional study

Author

Kaufmann, R L, Reiner, C S, Dietz, U A, Clavien, P A, Vonlanthen, R, Käser, S A; https://orcid.org/0000-0001-8692-5474, Kaufmann, R L, Reiner, C S, Dietz, U A, Clavien, P A, Vonlanthen, R, and Käser, S A; https://orcid.org/0000-0001-8692-5474

Abstract

AIM The prevalence and definition of diastasis recti abdominis (DRA) is under debate. This retrospective cross-sectional study evaluated the interrectal distance and the prevalence of DRA in computed tomography (CT) in an asymptomatic population. MATERIALS AND METHODS Patients undergoing CT scans for suspected appendicitis or kidney stones from 01/2016 to 12/2018 were screened retrospectively to participate. A study population with equal distribution according to gender and age (18-90 years) was generated (n = 329 patients) and the interrectal distance was measured at six reference points. RESULTS DRA (defined as > 2 cm at 3 cm above the umbilicus) was present in 57% of the population. The 80th percentile of the interrectal distance was 10 mm at the xiphoid (median 3 mm, 95% confidence interval (CI) 0-19 mm), 27 mm halfway from xiphoid to umbilicus (median 17 mm, 95% CI 0-39 mm), 34 mm at 3 cm above the umbilicus (median 22 mm, 95% CI 0-50 mm), 32 mm at the umbilicus (median 25 mm, 95% CI 0-45 mm), 25 mm at 2 cm below the umbilicus (median 14 mm, 95% CI 0-39 mm), and 4 mm halfway from umbilicus to pubic symphysis (median 0 mm, 95% CI 0-19 mm). In the multivariate analysis, higher age (p = 0.001), increased body mass index (p < 0.001), and parity (p < 0.037) were independent risk factors for DRA, while split xiphoid, tobacco abuse, and umbilical hernia were not. CONCLUSION The prevalence of DRA is much higher than commonly estimated (57%). The IRD 3 cm above the umbilicus may be considered normal up to 34 mm. To avoid over-treatment, the definition of DRA should be revised.

Published
2022

10. Distinct spin and orbital dynamics in Sr$_{2}$RuO$_{4}$

Author

Suzuki, H., Wang, L., Bertinshaw, J., Strand, H. U. R., Käser, S., Krautloher, M., Yang, Z., Wentzell, N., Parcollet, O., Jerzembeck, F., Kikugawa, N., Mackenzie, A. P., Georges, A., Hansmann, P., Gretarsson, H., and Keimer, B.

Subjects
Condensed Matter - Strongly Correlated Electrons, Strongly Correlated Electrons (cond-mat.str-el), FOS: Physical sciences
Abstract

The unconventional superconductor Sr$_2$RuO$_4$ has long served as a benchmark for theories of correlated-electron materials. The determination of the superconducting pairing mechanism requires detailed experimental information on collective bosonic excitations as potential mediators of Cooper pairing. We have used Ru $L_3$-edge resonant inelastic x-ray scattering to obtain comprehensive maps of the electronic excitations of Sr$_2$RuO$_4$ over the entire Brillouin zone. We observe multiple branches of dispersive spin and orbital excitations associated with distinctly different energy scales. The spin and orbital dynamical response functions calculated within the dynamical mean-field theory are in excellent agreement with the experimental data. Our results highlight the Hund metal nature of Sr$_{2}$RuO$_{4}$ and provide key information for the understanding of its unconventional superconductivity.

Published
2022
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14. Adenocarcinomas of the upper third of the rectum and the rectosigmoid junction seem to have similar prognosis as colon cancers even without radiotherapy, SAKK 40/87

Author

Käser, S., Froelicher, J., Li, Q., Müller, S., Metzger, U., Castiglione, M., Laffer, U., Maurer, C., Käser, S., Froelicher, J., Li, Q., Müller, S., Metzger, U., Castiglione, M., Laffer, U., and Maurer, C.

Abstract

Purpose: To investigate the prognosis of adenocarcinomas of the upper third of the rectum and the rectosigmoid-junction without radiotherapy. Methods: Patients from a multicenter randomized controlled trial from 1987-1993 on adjuvant chemotherapy for R0-resected colorectal cancers with stage I-III disease were retrospectively allocated: cancers of the lower two-thirds of the rectum (11cm or less from anal-verge, Group A, n = 205), of the upper-third of the rectum and rectosigmoid-junction (>11-20cm from anal-verge, Group B, n = 142), and of the colon (>20cm from anal-verge, Group C, n = 378). The total mesorectal excision (TME) technique had not been introduced yet. The adjuvant chemotherapy turned out to be ineffective. None of the patients received neoadjuvant or adjuvant radiotherapy. Results: The patients had a regular follow-up (median, 8.0years). The 5-year disease-free survival (DFS) rate was 0.54 (95%CI, 0.47-0.60) in Group A, 0.68 (95%CI, 0.60-0.75) in Group B, and 0.69 (95%CI, 0.64-0.74) in Group C. The 5-year overall survival (OS) rate was 0.64 (95%CI, 0.57-0.71) in Group A, 0.79 (95%CI, 0.71-0.85) in Group B, and 0.77 (95%CI, 0.73-0.81) in Group C. Compared with Group C, patients in Group A had a significantly worse OS (hazard ratio [HR] for death 2.10) and a worse DFS (HR for relapse/death 1.93), while patients in Group B had a similar OS (HR 1.12) and DFS (HR 1.07). Conclusions: Adenocarcinomas of the upper third of the rectum and the rectosigmoid-junction seem to have similar prognosis as colon cancers. Even for surgeons not familiar with the TME technique, preoperative radiotherapy may be avoided for most rectosigmoid cancers above 11cm from anal-verge.

Published
2021

15. Primary wound closure with a Limberg flap vs. secondary wound healing after excision of a pilonidal sinus: a multicentre randomised controlled study

Author

Käser, S., Zengaffinen, R., Uhlmann, M., Glaser, C., Maurer, C., Käser, S., Zengaffinen, R., Uhlmann, M., Glaser, C., and Maurer, C.

Abstract

Purpose: Off-midline procedures seem to be the best method of primary wound closure after excision of a pilonidal sinus. Primary wound closure with a Limberg flap was compared to secondary wound healing. Methods: From January 2006 to July 2012, 102 patients with given informed consent (mean age 28years, men 81%) who had excision of a pilonidal sinus in three hospitals in Switzerland were randomised to group L (Limberg flap, n = 51) or to group E (excision only, n = 51). Primary endpoint was duration of incapacity for work. Follow-up was at 3weeks and at 1year postoperative (95% follow-up). Results: Both groups were comparable with regard to patient characteristics. The median (range) operation time was 60 (30-80) min in group L vs. 30 (10-75) min in group E (p < 0.001). No significant differences were found in postoperative pain and painkiller intake; pain, percentage of patients at work and overall satisfaction at 3weeks postoperative; and overall duration of incapacity for work and overall satisfaction at 1-year follow-up. The complication rate was 49% in group L vs. 12% in group E (p < 0.001). Complications in group L were seroma (6%), wound dehiscence (45%), skin necrosis (10%), hematoma (6%), infection (4%) and recurrent disease (13%). Complications in group E were recurrent disease (6%) and wound healing disorder (6%). Conclusions: After excision of a pilonidal sinus, primary wound closure with a Limberg flap has no advantage over secondary wound healing. The main reason for this conclusion is the relatively high complication rate of primary wound closure with a Limberg flap.

Published
2021

20. Toward a Consensus on Centralization in Surgery

Author

Vonlanthen, René, Lodge, Peter, Barkun, Jeffrey S, et al, Käser, S A, Petrowsky, Henrik, Clavien, Pierre-Alain, University of Zurich, and Clavien, Pierre-Alain

Subjects
610 Medicine & health, 10217 Clinic for Visceral and Transplantation Surgery, 2746 Surgery
Published
2018

21. Could hyponatremia be a marker of anastomotic leakage after colorectal surgery? A single center analysis of 1,106 patients over 5years

Author

Käser, S., Nitsche, U., Maak, M., Michalski, C., Späth, C., Müller, T., Maurer, C., Janssen, K., Kleeff, J., Friess, H., Bader, F., Käser, S., Nitsche, U., Maak, M., Michalski, C., Späth, C., Müller, T., Maurer, C., Janssen, K., Kleeff, J., Friess, H., and Bader, F.

Abstract

Purpose: The aim of this study is to define the significance of hyponatremia as a marker of anastomotic leakage after colorectal surgery. Methods: All anastomoses in colorectal surgery performed at a single institution between July 2007 and July 2012 (n = 1,106) were retrospectively identified. Serum sodium levels and leukocyte values measured when an anastomotic leak was diagnosed by CT scan and/or surgical reintervention (n = 81) were compared to the values preferably on postoperative day 5 in the absence of an anastomotic leak (n = 1,025). Results: The leak rate in anastomoses of the rectum was 9.0%, while the leak rate of the other anastomoses was 5.4%. Mean serum sodium level was 138.8mmol/l in the group with an anastomotic leak and 140.5mmol/l in the group without. Hyponatremia (<136mmol/l) was present in 23% of patients in the group with an anastomotic leak and in 15% in the group without (p < 0.001). In multivariate analysis, leukocytes and serum sodium level remained as significant markers of an anastomotic leak. As a marker of an anastomotic leak, hyponatremia had a specificity of 93% and a sensitivity of 23%, while the presence of either leukocytosis or hyponatremia had a sensitivity of 68%, a specificity of 75%, a positive predictive value of 18%, and a negative predictive value of 97%. Conclusions: Hyponatremia could be a specific and relevant marker of anastomotic leakage after colorectal surgery. If hyponatremia and leukocytosis are present after colorectal surgery, anastomotic leakage should be suspected and a CT scan with rectal contrast dye is recommended.

Published
2019

23. The Impact of the Introduction of Total Mesorectal Excision on Local Recurrence Rate and Survival in Rectal Cancer: Long-Term Results

Author

Maurer, C., Renzulli, P., Kull, C., Käser, S., Mazzucchelli, L., Ulrich, A., Büchler, M., Maurer, C., Renzulli, P., Kull, C., Käser, S., Mazzucchelli, L., Ulrich, A., and Büchler, M.

Abstract

Purpose: To investigate the influence of the introduction of total mesorectal excision (TME) on local recurrence rate and survival in patients with rectal cancer. Methods: A total of 171 consecutive patients underwent anterior or abdominoperineal resection for primary rectal cancer. When the TME technique was introduced, the clinical setting, including the surgeons, remained the same. Group 1 (1993-95, n=53) underwent conventional surgery and group 2 (1995-2001, n=118) underwent TME. All patients were followed for 7years or until death. Results: Between the two groups, no statistically significant differences were present with regards to patient-, treatment-, or tumor-related characteristics apart from the time point of radiotherapy. The total local recurrence rates were 11 of 53 (20.8%) in group 1 and 7 of 118 (5.9%) in group 2, and the rates of isolated local recurrences were 6 of 53 (11.3%) in group 1 and 2 of 118 (1.7%) in group 2. Both differences were highly statistically significant. The disease-free survival in groups 1 and 2 was 60.4 and 65.3% at 5years, and 58.5 and 65.3% at 7years, respectively. Excluding patients with synchronous or metachronous distant metastasis from the analysis, both the disease-free survival and the cancer-specific survival were statistically significantly better in group 2 than in group 1. No statistically significant difference between the two groups was detected regarding the overall survival. Conclusions: The introduction of TME led to an impressive reduction of the local recurrence rate. Survival is mainly determined by the occurrence of distant metastasis, but TME seems to improve survival in patients without systemic disease

Published
2018

28. Venous Small Bowel Infarction: Intraoperative Laser Doppler Flowmetry Discriminates Critical Blood Supply and Spares Bowel Length

Author

Käser, S. A., Glauser, P. M., and Maurer, C. A.

Subjects
Article Subject
Abstract

Introduction. In mesenteric infarction due to arterial occlusion, laser Doppler flowmetry and spectrometry are known reliable noninvasive methods for measuring microvascular blood flow and oxygen utilisation. Case Presentation. As an innovation we used these methods in a patient with acute extensive mesenteric infarction due to venous occlusion, occurring after radical right hemicolectomy. Aiming to avoid short bowel syndrome, we spared additional 110 cm of small bowel, instead of leaving only 80 centimetres of clinically viable small bowel in situ. The pathological examination showed only 5 mm of vital mucosa to be left distal to the dissection margin. No further interventions were necessary. Conclusion. Laser doppler flowmetry and spectrometry are potentially powerful methods to assist the surgeon’s decision-making in critical venous mesenteric perfusion, thus having an important impact on clinical outcome.

Published
2012
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40. Adenocarcinomas of the upper third of the rectum and the rectosigmoid junction seem to have similar prognosis as colon cancers even without radiotherapy, SAKK 40/87

Author

Käser, S., Froelicher, J., Li, Q., Müller, S., Metzger, U., Castiglione, M., Laffer, U., Maurer, C., Käser, S., Froelicher, J., Li, Q., Müller, S., Metzger, U., Castiglione, M., Laffer, U., and Maurer, C.

Abstract

Purpose: To investigate the prognosis of adenocarcinomas of the upper third of the rectum and the rectosigmoid-junction without radiotherapy. Methods: Patients from a multicenter randomized controlled trial from 1987-1993 on adjuvant chemotherapy for R0-resected colorectal cancers with stage I-III disease were retrospectively allocated: cancers of the lower two-thirds of the rectum (11cm or less from anal-verge, Group A, n = 205), of the upper-third of the rectum and rectosigmoid-junction (>11-20cm from anal-verge, Group B, n = 142), and of the colon (>20cm from anal-verge, Group C, n = 378). The total mesorectal excision (TME) technique had not been introduced yet. The adjuvant chemotherapy turned out to be ineffective. None of the patients received neoadjuvant or adjuvant radiotherapy. Results: The patients had a regular follow-up (median, 8.0years). The 5-year disease-free survival (DFS) rate was 0.54 (95%CI, 0.47-0.60) in Group A, 0.68 (95%CI, 0.60-0.75) in Group B, and 0.69 (95%CI, 0.64-0.74) in Group C. The 5-year overall survival (OS) rate was 0.64 (95%CI, 0.57-0.71) in Group A, 0.79 (95%CI, 0.71-0.85) in Group B, and 0.77 (95%CI, 0.73-0.81) in Group C. Compared with Group C, patients in Group A had a significantly worse OS (hazard ratio [HR] for death 2.10) and a worse DFS (HR for relapse/death 1.93), while patients in Group B had a similar OS (HR 1.12) and DFS (HR 1.07). Conclusions: Adenocarcinomas of the upper third of the rectum and the rectosigmoid-junction seem to have similar prognosis as colon cancers. Even for surgeons not familiar with the TME technique, preoperative radiotherapy may be avoided for most rectosigmoid cancers above 11cm from anal-verge.

41. Primary wound closure with a Limberg flap vs. secondary wound healing after excision of a pilonidal sinus: a multicentre randomised controlled study

Author

Käser, S., Zengaffinen, R., Uhlmann, M., Glaser, C., Maurer, C., Käser, S., Zengaffinen, R., Uhlmann, M., Glaser, C., and Maurer, C.

Abstract

Purpose: Off-midline procedures seem to be the best method of primary wound closure after excision of a pilonidal sinus. Primary wound closure with a Limberg flap was compared to secondary wound healing. Methods: From January 2006 to July 2012, 102 patients with given informed consent (mean age 28years, men 81%) who had excision of a pilonidal sinus in three hospitals in Switzerland were randomised to group L (Limberg flap, n = 51) or to group E (excision only, n = 51). Primary endpoint was duration of incapacity for work. Follow-up was at 3weeks and at 1year postoperative (95% follow-up). Results: Both groups were comparable with regard to patient characteristics. The median (range) operation time was 60 (30-80) min in group L vs. 30 (10-75) min in group E (p < 0.001). No significant differences were found in postoperative pain and painkiller intake; pain, percentage of patients at work and overall satisfaction at 3weeks postoperative; and overall duration of incapacity for work and overall satisfaction at 1-year follow-up. The complication rate was 49% in group L vs. 12% in group E (p < 0.001). Complications in group L were seroma (6%), wound dehiscence (45%), skin necrosis (10%), hematoma (6%), infection (4%) and recurrent disease (13%). Complications in group E were recurrent disease (6%) and wound healing disorder (6%). Conclusions: After excision of a pilonidal sinus, primary wound closure with a Limberg flap has no advantage over secondary wound healing. The main reason for this conclusion is the relatively high complication rate of primary wound closure with a Limberg flap.

42. Could hyponatremia be a marker of anastomotic leakage after colorectal surgery? A single center analysis of 1,106 patients over 5years

Author

Käser, S., Nitsche, U., Maak, M., Michalski, C., Späth, C., Müller, T., Maurer, C., Janssen, K., Kleeff, J., Friess, H., Bader, F., Käser, S., Nitsche, U., Maak, M., Michalski, C., Späth, C., Müller, T., Maurer, C., Janssen, K., Kleeff, J., Friess, H., and Bader, F.

Abstract

Purpose: The aim of this study is to define the significance of hyponatremia as a marker of anastomotic leakage after colorectal surgery. Methods: All anastomoses in colorectal surgery performed at a single institution between July 2007 and July 2012 (n = 1,106) were retrospectively identified. Serum sodium levels and leukocyte values measured when an anastomotic leak was diagnosed by CT scan and/or surgical reintervention (n = 81) were compared to the values preferably on postoperative day 5 in the absence of an anastomotic leak (n = 1,025). Results: The leak rate in anastomoses of the rectum was 9.0%, while the leak rate of the other anastomoses was 5.4%. Mean serum sodium level was 138.8mmol/l in the group with an anastomotic leak and 140.5mmol/l in the group without. Hyponatremia (<136mmol/l) was present in 23% of patients in the group with an anastomotic leak and in 15% in the group without (p < 0.001). In multivariate analysis, leukocytes and serum sodium level remained as significant markers of an anastomotic leak. As a marker of an anastomotic leak, hyponatremia had a specificity of 93% and a sensitivity of 23%, while the presence of either leukocytosis or hyponatremia had a sensitivity of 68%, a specificity of 75%, a positive predictive value of 18%, and a negative predictive value of 97%. Conclusions: Hyponatremia could be a specific and relevant marker of anastomotic leakage after colorectal surgery. If hyponatremia and leukocytosis are present after colorectal surgery, anastomotic leakage should be suspected and a CT scan with rectal contrast dye is recommended.

43. The Impact of the Introduction of Total Mesorectal Excision on Local Recurrence Rate and Survival in Rectal Cancer: Long-Term Results

Author

Maurer, C., Renzulli, P., Kull, C., Käser, S., Mazzucchelli, L., Ulrich, A., Büchler, M., Maurer, C., Renzulli, P., Kull, C., Käser, S., Mazzucchelli, L., Ulrich, A., and Büchler, M.

Abstract

Purpose: To investigate the influence of the introduction of total mesorectal excision (TME) on local recurrence rate and survival in patients with rectal cancer. Methods: A total of 171 consecutive patients underwent anterior or abdominoperineal resection for primary rectal cancer. When the TME technique was introduced, the clinical setting, including the surgeons, remained the same. Group 1 (1993-95, n=53) underwent conventional surgery and group 2 (1995-2001, n=118) underwent TME. All patients were followed for 7years or until death. Results: Between the two groups, no statistically significant differences were present with regards to patient-, treatment-, or tumor-related characteristics apart from the time point of radiotherapy. The total local recurrence rates were 11 of 53 (20.8%) in group 1 and 7 of 118 (5.9%) in group 2, and the rates of isolated local recurrences were 6 of 53 (11.3%) in group 1 and 2 of 118 (1.7%) in group 2. Both differences were highly statistically significant. The disease-free survival in groups 1 and 2 was 60.4 and 65.3% at 5years, and 58.5 and 65.3% at 7years, respectively. Excluding patients with synchronous or metachronous distant metastasis from the analysis, both the disease-free survival and the cancer-specific survival were statistically significantly better in group 2 than in group 1. No statistically significant difference between the two groups was detected regarding the overall survival. Conclusions: The introduction of TME led to an impressive reduction of the local recurrence rate. Survival is mainly determined by the occurrence of distant metastasis, but TME seems to improve survival in patients without systemic disease

45. Normal width of the linea alba, prevalence, and risk factors for diastasis recti abdominis in adults, a cross-sectional study

Author

René Vonlanthen, Samuel A. Käser, C. S. Reiner, U. A. Dietz, P.-A. Clavien, R. L. Kaufmann, University of Zurich, and Käser, S A

Subjects
Adult, Percentile, medicine.medical_specialty, Adolescent, Diastasis, Muscle, Cross-sectional study, Umbilicus (mollusc), Population, Rectus Abdominis, Pubic symphysis, 610 Medicine & health, Young Adult, Pregnancy, Risk Factors, medicine, Prevalence, Humans, education, Herniorrhaphy, Aged, Retrospective Studies, 10217 Clinic for Visceral and Transplantation Surgery, Aged, 80 and over, education.field_of_study, business.industry, 10042 Clinic for Diagnostic and Interventional Radiology, Middle Aged, medicine.disease, Confidence interval, Umbilical hernia, Surgery, 2746 Surgery, medicine.anatomical_structure, Cross-Sectional Studies, Linea alba (abdomen), Female, business
Abstract

Aim The prevalence and definition of diastasis recti abdominis (DRA) is under debate. This retrospective cross-sectional study evaluated the interrectal distance and the prevalence of DRA in computed tomography (CT) in an asymptomatic population. Materials and methods Patients undergoing CT scans for suspected appendicitis or kidney stones from 01/2016 to 12/2018 were screened retrospectively to participate. A study population with equal distribution according to gender and age (18–90 years) was generated (n = 329 patients) and the interrectal distance was measured at six reference points. Results DRA (defined as > 2 cm at 3 cm above the umbilicus) was present in 57% of the population. The 80th percentile of the interrectal distance was 10 mm at the xiphoid (median 3 mm, 95% confidence interval (CI) 0–19 mm), 27 mm halfway from xiphoid to umbilicus (median 17 mm, 95% CI 0–39 mm), 34 mm at 3 cm above the umbilicus (median 22 mm, 95% CI 0–50 mm), 32 mm at the umbilicus (median 25 mm, 95% CI 0–45 mm), 25 mm at 2 cm below the umbilicus (median 14 mm, 95% CI 0–39 mm), and 4 mm halfway from umbilicus to pubic symphysis (median 0 mm, 95% CI 0–19 mm). In the multivariate analysis, higher age (p = 0.001), increased body mass index (p p Conclusion The prevalence of DRA is much higher than commonly estimated (57%). The IRD 3 cm above the umbilicus may be considered normal up to 34 mm. To avoid over-treatment, the definition of DRA should be revised.

Published
2022

46. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.

Author

Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, Deng Y, Devereux M, Ding X, Feig MF, Gao J, Glowacki DR, Gonzales JE 2nd, Hamaneh MB, Harder ED, Hayes RL, Huang J, Huang Y, Hudson PS, Im W, Islam SM, Jiang W, Jones MR, Käser S, Kearns FL, Kern NR, Klauda JB, Lazaridis T, Lee J, Lemkul JA, Liu X, Luo Y, MacKerell AD Jr, Major DT, Meuwly M, Nam K, Nilsson L, Ovchinnikov V, Paci E, Park S, Pastor RW, Pittman AR, Post CB, Prasad S, Pu J, Qi Y, Rathinavelan T, Roe DR, Roux B, Rowley CN, Shen J, Simmonett AC, Sodt AJ, Töpfer K, Upadhyay M, van der Vaart A, Vazquez-Salazar LI, Venable RM, Warrensford LC, Woodcock HL, Wu Y, Brooks CL 3rd, Brooks BR, and Karplus M

Abstract

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

Published
2024
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47. Numerical Accuracy Matters: Applications of Machine Learned Potential Energy Surfaces.

Author

Käser S and Meuwly M

Abstract

The role of numerical accuracy in training and evaluating neural network-based potential energy surfaces is examined for different experimental observables. For observables that require third- and fourth-order derivatives of the potential energy with respect to Cartesian coordinates single-precision arithmetics as is typically used in ML-based approaches is insufficient and leads to roughness of the underlying PES as is explicitly demonstrated. Increasing the numerical accuracy to double-precision gives a smooth PES with higher-order derivatives that are numerically stable and yield meaningful anharmonic frequencies and tunneling splitting as is demonstrated for H 2 CO and malonaldehyde. For molecular dynamics simulations, which only require first-order derivatives, single-precision arithmetics appears to be sufficient, though.

Published
2024
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48. The first HyDRA challenge for computational vibrational spectroscopy.

Author

Fischer TL, Bödecker M, Schweer SM, Dupont J, Lepère V, Zehnacker-Rentien A, Suhm MA, Schröder B, Henkes T, Andrada DM, Balabin RM, Singh HK, Bhattacharyya HP, Sarma M, Käser S, Töpfer K, Vazquez-Salazar LI, Boittier ED, Meuwly M, Mandelli G, Lanzi C, Conte R, Ceotto M, Dietrich F, Cisternas V, Gnanasekaran R, Hippler M, Jarraya M, Hochlaf M, Viswanathan N, Nevolianis T, Rath G, Kopp WA, Leonhard K, and Mata RA

Abstract

Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggregates in close to ideal conditions for the benchmarking of quantum chemical approaches. The low temperatures achieved as well as the absence of environment effects allow for a direct comparison between computed and experimental spectra. This provides potential benchmarking data which can be revisited to hone different computational techniques, and it allows for the critical analysis of procedures under the setting of a blind challenge. In the latter case, the final result is unknown to modellers, providing an unbiased testing opportunity for quantum chemical models. In this work, we present the spectroscopic and computational results for the first HyDRA blind challenge. The latter deals with the prediction of water donor stretching vibrations in monohydrates of organic molecules. This edition features a test set of 10 systems. Experimental water donor OH vibrational wavenumbers for the vacuum-isolated monohydrates of formaldehyde, tetrahydrofuran, pyridine, tetrahydrothiophene, trifluoroethanol, methyl lactate, dimethylimidazolidinone, cyclooctanone, trifluoroacetophenone and 1-phenylcyclohexane- cis -1,2-diol are provided. The results of the challenge show promising predictive properties in both purely quantum mechanical approaches as well as regression and other machine learning strategies.

Published
2023
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49. A Msp1-containing complex removes orphaned proteins in the mitochondrial outer membrane of T. brucei .

Author

Gerber M, Suppanz I, Oeljeklaus S, Niemann M, Käser S, Warscheid B, Schneider A, and Dewar CE

Subjects
Animals, Humans, Mitochondrial Membranes, Membrane Proteins, Proteasome Endopeptidase Complex, Protein Subunits, ATPases Associated with Diverse Cellular Activities genetics, Proteomics, Saccharomyces cerevisiae genetics
Abstract

The AAA-ATPase Msp1 extracts mislocalised outer membrane proteins and thus contributes to mitochondrial proteostasis. Using pulldown experiments, we show that trypanosomal Msp1 localises to both glycosomes and the mitochondrial outer membrane, where it forms a complex with four outer membrane proteins. The trypanosome-specific pATOM36 mediates complex assembly of α-helically anchored mitochondrial outer membrane proteins such as protein translocase subunits. Inhibition of their assembly triggers a pathway that results in the proteasomal digestion of unassembled substrates. Using inducible single, double, and triple RNAi cell lines combined with proteomic analyses, we demonstrate that not only Msp1 but also the trypanosomal homolog of the AAA-ATPase VCP are implicated in this quality control pathway. Moreover, in the absence of VCP three out of the four Msp1-interacting mitochondrial proteins are required for efficient proteasomal digestion of pATOM36 substrates, suggesting they act in concert with Msp1. pATOM36 is a functional analog of the yeast mitochondrial import complex complex and possibly of human mitochondrial animal-specific carrier homolog 2, suggesting that similar mitochondrial quality control pathways linked to Msp1 might also exist in yeast and humans., (© 2023 Gerber et al.)

Published
2023
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50. PhysNet meets CHARMM: A framework for routine machine learning/molecular mechanics simulations.

Author

Song K, Käser S, Töpfer K, Vazquez-Salazar LI, and Meuwly M

Abstract

Full-dimensional potential energy surfaces (PESs) based on machine learning (ML) techniques provide a means for accurate and efficient molecular simulations in the gas and condensed phase for various experimental observables ranging from spectroscopy to reaction dynamics. Here, the MLpot extension with PhysNet as the ML-based model for a PES is introduced into the newly developed pyCHARMM application programming interface. To illustrate the conception, validation, refining, and use of a typical workflow, para-chloro-phenol is considered as an example. The main focus is on how to approach a concrete problem from a practical perspective and applications to spectroscopic observables and the free energy for the -OH torsion in solution are discussed in detail. For the computed IR spectra in the fingerprint region, the computations for para-chloro-phenol in water are in good qualitative agreement with experiment carried out in CCl4. Moreover, relative intensities are largely consistent with experimental findings. The barrier for rotation of the -OH group increases from ∼3.5 kcal/mol in the gas phase to ∼4.1 kcal/mol from simulations in water due to favorable H-bonding interactions of the -OH group with surrounding water molecules., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

Published
2023
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