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It is our real pain to write this article, remembering years of friendship and scientific collaboration with Stefan Sokołowski, who passed away on the 24th of June 2024. He was a strong man in his faith and convictions, a kind and helpful friend, attentive and open-minded in discussions, creative, profound and sophisticated in understanding the flow of life and science. He left an unforgettable mark on our hearts and personal memories. His way of thinking left an imprint on students, young scientists and co-workers. We accompany all that with warm farewell applause as an appreciation of Stefan’s way and effects throughout his life.

The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly. Molecular dynamics simulation, as an appropriate computational tool for studying the hydration shell of proteins, is also discussed. The concept of protein surfaces with fractal dimensions is elaborated. We finish by exposing an experimental (using small angle X-ray scattering) and a computer simulation case study, which are meant as demonstrations of the possibilities we have at hand for investigating the delicate interfaces that connect (and divide) protein molecules and the neighboring electrolyte solution.

We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-methanol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient conditions. The SPC/E and TIP4P/Ew water models are used in combination with the OPLS united atom modelling for methanol. Changes of the average number of hydrogen bonds between particles of different species and of the fractions of differently bonded molecules are put in correspondence with the behavior of excess mixing volume and enthalpy, of self-diffusion coefficients and rotational relaxation times. From the detailed analyses of the results obtained in this work, we conclude that an improvement of the description of an ample set of properties of water-methanol mixtures can possibly be reached, if a more sophisticated, carefully parameterized, e.g., all atom, model for methanol is used. Moreover, exploration of parametrization of the methanol force field, with simultaneous application of different combination rules for methanol-water cross interactions, is required.

Following a fairly comprehensive study on popular interaction potentials of water (Pusztai et al 2008, J. Chem. Phys., 129 184103), here two more recent, polarizable potential sets, SWM4-DP (Lamoureux et al., Chem. Phys. Lett., 2006, 418 245) and BK3 (Kiss et al. J. Chem. Phys., 2013, 138 204507) are compared to the TIP4P-2005 water potential (Abascal et al., J. Chem. Phys., 2005, 123 234505) that had appeared the most favoravble previously. The basis of comparison was the compatibility with results of neutron and X-ray diffraction experiments on pure water, using the scheme applied by Pusztai et al. (2008). The scheme combines the experimental total scattering structure factors (TSSF) and partial radial distribution functions (PRDF) from molecular dynamics simulations in a single structural model. Goodness-of-fit values to the O-O, O-H and H-H simulated PRDF-s and to the experimental neutron and X-ray TSSF provided a measure that can characterize the level of consistency between interaction potentials and diffraction experiments. Among the sets of partial RDF-s investigated here, the ones corresponding to the SWM4-DP potential parameters have proven to be the most consistent with the particular diffraction results taken for the present study, by a hardly significant margin ahead of BK3. Perhaps more importantly, it is shown that the three sets of potential parameters produce nearly equivalent PRDF-s that may all be made consistent with diffraction data at a very high level. The largest differences can be detected in terms of the O-O partial radial distribution function.

There are various routes for deriving partial radial distribution functions of disordered systems from experimental diffraction (and/or EXAFS) data. Due to limitations and errors of experimental data, as well as to imperfections of the evaluation procedures, it is of primary importance to confirm that the end result (partial radial distribution functions) and the primary information (diffraction data) are consistent with each other. We introduce a simple approach, based on Reverse Monte Carlo modelling, that is capable of assessing this dilemma. As a demonstration, we use the most frequently cited set of "experimental" partial radial distribution functions on liquid water and investigate whether the 3 partials (O-O, O-H and H-H) are consistent with the total structure factor of pure liquid D2O from neutron diffraction and that of H2O from X-ray diffraction. We find that while neutron diffraction on heavy water is in full agreement with all the 3 partials, the addition of X-ray diffraction data clearly shows problems with the O-O partial radial distribution function. We suggest that the approach introduced here may also be used to establish whether partial radial distribution functions obtained from statistical theories of the liquid state are consistent with the measured structure factors.

Background: The aim of this study was to compare the extent of pathologic response in patients with HER2-positive (HER2+) breast cancer treated with standard neoadjuvant chemotherapy, with or without trastuzumab (H), according to hormone receptor (HR) status. Patients and methods: We included 199 patients with HER2+ breast cancer from three successive cohorts of neo-adjuvant chemotherapy on the basis of paclitaxel (Taxol) (P) administered weekly (w) or three weekly (3-w), followed by 5-fluorouracil (F), doxorubicin (A) or epirubicin (E), and cyclophosphamide (C). Residual cancer burden (RCB) was determined from pathologic review of the primary tumor and lymph nodes and was classified as pathologic complete response (pCR) or minimal (RCB-I), moderate (RCB-II), or extensive (RCB-III) residual disease. Results: In HR-positive (HR+) cancers, a higher rate of pathologic response (pCR/RCB-I) was observed with concurrent H + 3-wP/FEC (73%) than with 3-wP/FEC (34%, P = 0.002) or wP/FAC (47%; P = 0.02) chemotherapy alone. In HR-negative (HR−) cancers, there were no significant differences in the rate of pathologic response (pCR/RCB-I) from 3-wP/FAC (50%), wP/FAC (68%), or concurrent H + 3-wP/FEC (72%). Conclusions: Patients with HR+/HER2+ breast cancer obtained significant benefit from addition of trastuzumab to P/FEC chemotherapy; pathologic response rate was similar to that seen in HR−/HER2+ breast cancers. [ABSTRACT FROM AUTHOR]

Background: Novel molecular therapies for metastatic breast cancer (MBC) are necessary to improve the dismal prognosis of this condition. Imatinib mesylate (Gleevec®) inhibits several protein tyrosine kinases, including platelet-derived growth factor receptor (PDGFR) and c-kit, which are preferentially expressed in tumor cells. We tested the activity of imatinib mesylate in MBC with overexpression of PDGFR or c-kit. Additionally, we sought to determine the biological correlates and immunomodulatory effects. Patients and methods: Thirteen patients were treated with Imatinib administered orally at 400 mg p.o. b.i.d. (800 mg/day), until disease progression. All patients demonstrated PDGFR-β overexpression and none showed c-kit expression. Results: No objective responses were observed among the 13 patients treated in an intention-to-treat analysis. All patients experienced disease progression, with a median time to progression of 1.2 months. Twelve patients have died, and the median overall survival was 7.7 months. No patient had a serious adverse event. Imatinib therapy had no effect on the plasma levels of the angiogenesis-related cytokines, vascular endothelial growth factor, PDGF, b-fibroblast growth factor, and E-selectin. Immune studies showed imatinib inhibits interferon-γ production by TCR-activated CD4+ T cells. Conclusion: Imatinib as a single agent has no clinical activity in PDGFR-overexpressing MBC and has potential immunosuppressive effects. [ABSTRACT FROM AUTHOR]

Background: AKT phosphorylation is a critical step in the activation of growth factor receptors and can mediate tumor resistance to anthracyclines. We evaluated the expression patterns and predictive value of phosphorylated AKT (pAKT) in breast cancer tissues. Patients and methods: pAKT expression was assessed by immunohistochemistry in 823 tumors from patients with early breast cancer enrolled in two randomized trials. The distribution of pAKT expression was correlated with HER2 and epidermal growth factor receptor (EGFR) expression. The predictive value of pAKT for the efficacy of adjuvant chemotherapy was determined by test for interaction. Results: pAKT, EGFR, and HER2 were expressed in 119 of 781 (15%), 118 of 758 (16%), and 99 of 775 (13%) assessable tumors. Staining was positive for pAKT in 28 of 99 (28%) and 90 of 676 (13%) HER2+ and HER2− tumors (P P = 0.49). A positive staining for pAKT did not correlate with prognosis (P = 0.94), and did not predict the resistance to anthracyclines (test for interaction, P = 0.70). Conclusions: AKT phosphorylation is associated with HER2 expression but not EGFR expression in patients with early breast cancer. pAKT is not predictive for the efficacy of anthracycline-based adjuvant chemotherapy. [ABSTRACT FROM AUTHOR]

Background: We examined if inclusion of a taxane and more prolonged preoperative chemotherapy improves pathologic complete response (pCR) rate in estrogen receptor (ER)-positive breast cancer compared with three to four courses of 5-fluorouracil, doxorubicin, cyclophosphamide (FAC). Patients and methods: Pooled analysis of results from seven consecutive neo-adjuvant chemotherapy trials including 1079 patients was carried out. These studies were conducted at MD Anderson Cancer Center from 1974 to 2001. Four hundred and twenty-six (39.5%) patients received taxane-based neo-adjuvant therapy. pCR rates and survival times were analyzed as a function of chemotherapy regimen and ER status. Multivariate logistic and Cox regression analysis were carried out to identify variables associated with pCR and survival. Results: Patients with ER-negative cancer had higher overall pCR rate than patients with ER-positive tumors (20.1% versus 4.9%, P < 0.001). In ER-negative patients, the pCR rates were 29% and 15% with and without a taxane (P < 0.001). In ER-positive patients, the pCR rates were 8.8% and 2.0% with and without a taxane (P < 0.001). In multivariate analysis, clinical tumor size (P < 0.001), ER-negative status (P < 0.001) and inclusion of a taxane (P = 0.01) were independently associated with pCR. For patients with pCR, survival was similar regardless of ER status or the type of regimen that induced pCR. Conclusion: pCR rates increased for patients with both ER-positive and ER-negative tumors as regimens started to include a taxane and became longer. This indicates that a subset of patients with ER-positive breast cancer benefits from more aggressive chemotherapy, similarly to patients with ER-negative tumors. [ABSTRACT FROM AUTHOR]