Optimization problems in electron microscopy of single particles

The final publication is available at Springer via http://dx.doi.org/10.1007/s10479-006-0078-8Electron Microscopy is a valuable tool for the elucidation of the three-dimensional structure of macromolecular complexes. Knowledge about the macromolecular structure provides important information about its function and how it is carried out. This work addresses the issue of three-dimensional reconstruction of biological macromolecules from electron microscopy images. In particular, it focuses on a methodology known as “single-particles” and makes a thorough review of all those steps that can be expressed as an optimization problem. In spite of important advances in recent years, there are still unresolved challenges in the field that offer an excellent testbed for new and more powerful optimization techniques.We acknowledge partial support from the “Comunidad Autónoma de Madrid” through grants CAM-07B-0032-2002, GR/SAL/0653/2004 and GR/SAL/0342/2004, the “Comisión Interministerial de Ciencia yTecnologia” of Spain through grants BIO2001-1237, BIO2001-4253-E, BIO2001-4339-E, BIO2002- 10855-E, BFU2004-00217/BMC, the Spanish FIS grant (G03/185), the European Union through grants QLK2- 2000-00634, QLRI-2000-31237, QLRT-2000-0136, QLRI-2001-00015, FP6-502828 and the NIH through grant HL70472. Alberto Pascual and Roberto Marabini acknowledge support by the Spanish Ramon y Cajal Program

On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy

This work was funded by the Spanish Ministerio de Economía y Competividad through grants BFU2009-09331, BIO2010-16566, ACI2009-1022, ACI2010-1088 and AIC-A- 2011-0638, by the Comunidad Autonoma de Madrid through grant S2010/BMD-2305, by NFS grant No. 1114901 and by the Spanish National Institute of Bioinformatics (a project funded by the Instituto de Salud Carlos III). This work was conducted using the Protégé resource, which is supported by grant LM007885 from the United States National Library of Medicine. COSS is a Ramón y Cajal researcher financed by the European Social Fund and the Ministerio de Economía y Competitividad. JV is a Juan de la Cierva Postdoctoral Fellow (JCI-2011-10185). This work was funded by Instruct, which is part of the European Strategy Forum on Research Infrastructures (ESFRI) and is supported by national member subscriptions

Two-step interferometry by a regularized optical flow algorithm

A two-step phase-shifting method, that can demodulate open-and closed-fringed patterns without local sign ambiguity is presented. The proposed method only requires a constant phase-shift between the two interferograms. This phase-shift does not need to be known and can take any value inside the range (0, 2 π), excluding the singular case where it corresponds to π. The proposed method is based on determining first the fringe direction map by a regularized optical flow algorithm. After that, we apply the spiral phase transform (SPT) to one of the fringe patterns and we determine its quadrature signal using the previously determined direction. The proposed technique has been applied to simulated and experimental interferograms obtaining satisfactory results. A complete MATLAB software package is provided in [http://goo.gl/Snnz7]

Consistent and elastic registration of histological sections using vector-spline regularization

The final publication is available at Springer via http://dx.doi.org/10.1007/11889762_8Revised Papers on Second International ECCV Workshop, CVAMIA 2006 Graz, Austria, May 12, 2006Here we present a new image registration algorithm for the alignment of histological sections that combines the ideas of B-spline based elastic registration and consistent image registration, to allow simultaneous registration of images in two directions (direct and inverse). In principle, deformations based on B-splines are not invertible. The consistency term overcomes this limitation and allows registration of two images in a completely symmetric way. This extension of the elastic registration method simplifies the search for the optimum deformation and allows registering with no information about landmarks or deformation regularization. This approach can also be used as the first step to solve the problem of group-wise registration.Ignacio Arganda-Carreras is being supported by a predoctoral FPI-CAM fellow- ship since October 2003. Carlos Ortiz-de-Solorzano is supported by a Ramon y Cajal (Spanish Ministry of Education and Science ryc-2004-002353) and a Marie Curie International Reintegration Grant (FP6-518688). Jan Kybic was sponsored by the Czech Ministery of Education under project number MSM210000012. Par- tial support is acknowledged to Comunidad de Madrid through grant GR/SAL/0234, to Instituto de Salud Carlos III-Fondo de Investigaciones Sanitarias (FIS) through the IM3 Network and grant 040683 and to the Plan Nacional de Investigación Científica, Desarrollo e Innovación Tecnológica (I+D+I)

A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis

Single particle analysis (SPA) in cryo-electron microscopy (cryo-EM) is highly used to obtain the near-atomic structure of biological macromolecules. The current methods allow users to produce high-resolution maps from many samples. However, there are still challenging cases that require extra processing to obtain high resolution. This is the case when the macromolecule of the sample is composed of different components and we want to focus just on one of them. For example, if the macromolecule is composed of several flexible subunits and we are interested in a specific one, if it is embedded in a viral capsid environment, or if it has additional components to stabilize it, such as nanodiscs. The signal from these components, which in principle we are not interested in, can be removed from the particles using a projection subtraction method. Currently, there are two projection subtraction methods used in practice and both have some limitations. In fact, after evaluating their results, we consider that the problem is still open to new solutions, as they do not fully remove the signal of the components that are not of interest. Our aim is to develop a new and more precise projection subtraction method, improving the performance of state-of-the-art methods. We tested our algorithm with data from public databases and an in–house data set. In this work, we show that the performance of our algorithm improves the results obtained by others, including the localization of small ligands, such as drugs, whose binding location is unknown a prioriThe authors acknowledge the economic support from MICIN to the Instruct Image Processing Center (I2PC) as part of the Spanish participation in Instruct-ERIC, the European Strategic Infrastructure Project (ESFRI) in Structural Biology. Grant PID2019-104757RB-I00 is funded by MCIN/AEI/ 10.13039/ 501100011033 and “ERDF A way of making Europe”, by the European Union. The “Comunidad Autónoma de Madrid” through Grant S2022/BMD-7232, the European Union (EU) and Horizon 2020 through grant HighResCells (ERC-2018-SyG, Proposal: 810057). The authors also acknowledge grant PID2019-104098 GB-I00/AEI/10.13039/501100011033, cofunded by the Spanish State Research Agency and the European Regional Development and grant 2023AEP082 by Agencia Estatal CSIC. Ruben Sanchez-Garcia is funded by an Astex Pharmaceuticals Sustaining Innovation Post-Doctoral Awar

Fringe pattern denoising by image dimensionality reduction

Noise is a key problem in fringe pattern processing, especially in single frame demodulation of interferograms. In this work, we propose to filter the pattern noise using a straightforward, fast and easy to implement denoising method, which is based on a dimensionality reduction approach, in the sense of image rank reduction. The proposed technique has been applied to simulated and experimental ESPI interferograms obtaining satisfactory results

Circadian Genes as Therapeutic Targets in Pancreatic Cancer

JL was supported by the Nicolás Monardes Program from the Andalusian Health Service (C-0033-2015). This work was supported by a research grant from the Instituto de Salud Carlos III-FEDER (PI18/01947).Pancreatic cancer is one of the most lethal cancers worldwide due to its symptoms, early metastasis, and chemoresistance. Thus, the mechanisms contributing to pancreatic cancer progression require further exploration. Circadian rhythms are the daily oscillations of multiple biological processes regulated by an endogenous clock. Several evidences suggest that the circadian clock may play an important role in the cell cycle, cell proliferation and apoptosis. In addition, timing of chemotherapy or radiation treatment can influence the efficacy and toxicity treatment. Here, we revisit the studies on circadian clock as an emerging target for therapy in pancreatic cancer. We highlight those potential circadian genes regulators that are commonly affected in pancreatic cancer according to most recent reports.Nicolás Monardes Program from the Andalusian Health Service (C-0033-2015)Instituto de Salud Carlos III-FEDER (PI18/01947

Variability and power enhancement of current controlled resistive switching devices

Producción CientíficaIn this work, the unipolar resistive switching behaviour of Ni/HfO2/Si(n+) devices is studied. The structures are characterized using both current and voltage sweeps, with the device resistance and its cycle-to-cycle variability being analysed in each case. Experimental measurements indicate a clear improvement on resistance states stability when using current sweeps to induce both set and reset processes. Moreover, it has been found that using current to induce these transitions is more efficient than using voltage sweeps, as seen when analysing the device power consumption. The same results are obtained for devices with a Ni top electrode and a bilayer or pentalayer of HfO2/Al2O3 as dielectric. Finally, kinetic Monte Carlo and compact modelling simulation studies are performed to shed light on the experimental results.Junta de Andalucía - FEDER (B-TIC-624-UGR20)Consejo Superior de Investigaciones Científicas (CSIC) (project 20225AT012)Ramón y Cajal (grant RYC2020-030150-I

Relationship between Aldehyde Dehydrogenase, PD-L1 and Tumor-Infiltrating Lymphocytes with Pathologic Response and Survival in Breast Cancer

[EN] Aldehyde dehydrogenase 1A1 (ALDH1A1) is a cancer stem cell (CSC) marker related to clinical outcomes in breast cancer (BC). The aim of this study was to analyze the relationship between ALDH1A1, programmed death ligand 1 (PD-L1) and tumor-infiltrating lymphocytes (TILs) in triple negative (TN) and human epidermal growth factor receptor 2-positive (HER2+) BC tumors, and its association with clinicopathological characteristics and outcomes. A retrospective, historical cohort study of patients diagnosed with early or locally advanced BC treated with neoadjuvant chemotherapy was conducted. ALDH1A1, PD-L1 expression and TILs were assessed using immunohistochemistry. A total of 75 patients were analyzed (42.7% TN, 57.3% HER2+ tumors). ALDH1A1+ was related to HTILs (p = 0.005) and PD-L1+ tumors (p = 0.004). ALDH1A1+ tumors presented higher CD3+ (p = 0.008), CD4+ (p = 0.005), CD8+ (p = 0.003) and CD20+ (p = 0.006) TILs. ALDH1A1+ (p = 0.018), PD-L1+ (p = 0.004) and HTILs (p < 0.001) were related to smaller tumors. ALDH1A1+ was related to pathologic complete response (pCR) (p = 0.048). At the end of the follow-up (54.4 [38.3–87.6] months), 47 patients (62.7%) remained disease-free, and 20 (26.7%) had died. HTILs were related to improved disease-free survival (p = 0.027). ALDH1A1+ was related to PD-L1+ and HITLs, that might be related to higher pCR rates with neoadjuvant therapy.S

Malignancy following heart transplantation: differences in incidence and prognosis between sexes – a multicenter cohort study

[Abstract] Male patients are at increased risk for developing malignancy postheart transplantation (HT); however, real incidence and prognosis in both genders remain unknown. The aim of this study was to assess differences in incidence and mortality related to malignancy between genders in a large cohort of HT patients. Incidence and mortality rates were calculated for all tumors, skin cancers (SCs), lymphoma, and nonskin solid cancers (NSSCs) as well as survival since first diagnosis of neoplasia. 5865 patients (81.6% male) were included. Total incidence rates for all tumors, SCs, and NSSCs were lower in females [all tumors: 25.7 vs. 44.8 per 1000 person‐years; rate ratio (RR) 0.68, (0.60–0.78), P < 0.001]. Mortality rates were also lower in females for all tumors [94.0 (77.3–114.3) vs. 129.6 (120.9–138.9) per 1000 person‐years; RR 0.76, (0.62–0.94), P = 0.01] and for NSSCs [125.0 (95.2–164.0) vs 234.7 (214.0–257.5) per 1000 person‐years; RR 0.60 (0.44–0.80), P = 0.001], albeit not for SCs or lymphoma. Female sex was associated with a better survival after diagnosis of malignancy [log‐rank p test = 0.0037; HR 0.74 (0.60–0.91), P = 0.004]. In conclusion, incidence of malignancies post‐HT is higher in males than in females, especially for SCs and NSSCs. Prognosis after cancer diagnosis is also worse in males