"Self-Designed Simulation-Based Laparoscopic Training Program for Urology Residents: Results After 6 Years of Experience".

Introduction: Learning laparoscopy (LAP) is challenging and requires different skills to conventional open surgery. There is a recognized need for a standardized laparoscopic training framework within urology to overcome these difficulties and to shift learning curve from patient to skills laboratory. Simulation-based training has been widely commented, but implementation in real day practice is lacking. We present our "LAP training program for residents". Material: Between 2017 and 2022, 11 residents participated in our self-designed program: Theoretical: (Moodle platform) basic knowledge and multimedia content for initiation into LAP. Evaluated through online exam. Practical: exercises for LAP skills acquisition were proposed and encouraged residents' practice in a box trainer available and experimental surgery sessions on a porcine model. On-site E-BLUS (European Basic Laparoscopic Urologic Skills) examination was performed annually. Feedback was obtained through an anonymous online survey. Results: All residents positively evaluated the program. Theoretical: 82% passed the online exam. The most valued topics: LAP in special clinical situations, complications, instruments, and configuration of the operating room (OR). Practical: all residents increased dry-lab box practices. A total of 23 experimental surgical sessions were carried out. For 64%, simulation in the experimental OR was a necessary complement to achieve laparoscopic skills and allowed them to feel more confident. Forty-five percent considered it essential to improve their surgical technique. E-BLUS evaluation was valued as a means to achieve dexterity and safer surgery by 90%. Reduction in time and errors were observed through time, although only 2 passed the E-BLUS. Conclusion: Our program for learning LAP includes the acquisition of knowledge, training of basic skills and surgical technique in a safe environment, as well as an objective evaluation. Encouraged practice of basic skills and surgical technique simulation and improved objective evaluation. It is structured, reproducible, systematic and has been positively valued, although it requires commitment for success.

EventPointer 3.0: flexible and accurate splicing analysis that includes studying the differential usage of protein-domains.

Alternative splicing (AS) plays a key role in cancer: all its hallmarks have been associated with different mechanisms of abnormal AS. The improvement of the human transcriptome annotation and the availability of fast and accurate software to estimate isoform concentrations has boosted the analysis of transcriptome profiling from RNA-seq. The statistical analysis of AS is a challenging problem not yet fully solved. We have included in EventPointer (EP), a Bioconductor package, a novel statistical method that can use the bootstrap of the pseudoaligners. We compared it with other state-of-the-art algorithms to analyze AS. Its performance is outstanding for shallow sequencing conditions. The statistical framework is very flexible since it is based on design and contrast matrices. EP now includes a convenient tool to find the primers to validate the discoveries using PCR. We also added a statistical module to study alteration in protein domain related to AS. Applying it to 9514 patients from TCGA and TARGET in 19 different tumor types resulted in two conclusions: i) aberrant alternative splicing alters the relative presence of Protein domains and, ii) the number of enriched domains is strongly correlated with the age of the patients.

Identifying Lethal Dependencies with HUGE Predictive Power.

Recent functional genomic screens­such as CRISPR-Cas9 or RNAi screening­have fostered a new wave of targeted treatments based on the concept of synthetic lethality. These approaches identified LEthal Dependencies (LEDs) by estimating the effect of genetic events on cell viability. The multiple-hypothesis problem is related to a large number of gene knockouts limiting the statistical power of these studies. Here, we show that predictions of LEDs from functional screens can be dramatically improved by incorporating the "HUb effect in Genetic Essentiality" (HUGE) of gene alterations. We analyze three recent genome-wide loss-of-function screens­Project Score, CERES score and DEMETER score­identifying LEDs with 75 times larger statistical power than using state-of-the-art methods. Using acute myeloid leukemia, breast cancer, lung adenocarcinoma and colon adenocarcinoma as disease models, we validate that our predictions are enriched in a recent harmonized knowledge base of clinical interpretations of somatic genomic variants in cancer (AUROC > 0.87). Our approach is effective even in tumors with large genetic heterogeneity such as acute myeloid leukemia, where we identified LEDs not recalled by previous pipelines, including FLT3-mutant genotypes sensitive to FLT3 inhibitors. Interestingly, in-vitro validations confirm lethal dependencies of either NRAS or PTPN11 depending on the NRAS mutational status. HUGE will hopefully help discover novel genetic dependencies amenable for precision-targeted therapies in cancer. All the graphs showing lethal dependencies for the 19 tumor types analyzed can be visualized in an interactive tool.

DrugSniper, a Tool to Exploit Loss-Of-Function Screens, Identifies CREBBP as a Predictive Biomarker of VOLASERTIB in Small Cell Lung Carcinoma (SCLC).

The development of predictive biomarkers of response to targeted therapies is an unmet clinical need for many antitumoral agents. Recent genome-wide loss-of-function screens, such as RNA interference (RNAi) and CRISPR-Cas9 libraries, are an unprecedented resource to identify novel drug targets, reposition drugs and associate predictive biomarkers in the context of precision oncology. In this work, we have developed and validated a large-scale bioinformatics tool named DrugSniper, which exploits loss-of-function experiments to model the sensitivity of 6237 inhibitors and predict their corresponding biomarkers of sensitivity in 30 tumor types. Applying DrugSniper to small cell lung cancer (SCLC), we identified genes extensively explored in SCLC, such as Aurora kinases or epigenetic agents. Interestingly, the analysis suggested a remarkable vulnerability to polo-like kinase 1 (PLK1) inhibition in CREBBP-mutant SCLC cells. We validated this association in vitro using four mutated and four wild-type SCLC cell lines and two PLK1 inhibitors (Volasertib and BI2536), confirming that the effect of PLK1 inhibitors depended on the mutational status of CREBBP. Besides, DrugSniper was validated in-silico with several known clinically-used treatments, including the sensitivity of Tyrosine Kinase Inhibitors (TKIs) and Vemurafenib to FLT3 and BRAF mutant cells, respectively. These findings show the potential of genome-wide loss-of-function screens to identify new personalized therapeutic hypotheses in SCLC and potentially in other tumors, which is a valuable starting point for further drug development and drug repositioning projects.

ISOGO: Functional annotation of protein-coding splice variants.

The advent of RNA-seq technologies has switched the paradigm of genetic analysis from a genome to a transcriptome-based perspective. Alternative splicing generates functional diversity in genes, but the precise functions of many individual isoforms are yet to be elucidated. Gene Ontology was developed to annotate gene products according to their biological processes, molecular functions and cellular components. Despite a single gene may have several gene products, most annotations are not isoform-specific and do not distinguish the functions of the different proteins originated from a single gene. Several approaches have tried to automatically annotate ontologies at the isoform level, but this has shown to be a daunting task. We have developed ISOGO (ISOform + GO function imputation), a novel algorithm to predict the function of coding isoforms based on their protein domains and their correlation of expression along 11,373 cancer patients. Combining these two sources of information outperforms previous approaches: it provides an area under precision-recall curve (AUPRC) five times larger than previous attempts and the median AUROC of assigned functions to genes is 0.82. We tested ISOGO predictions on some genes with isoform-specific functions (BRCA1, MADD,VAMP7 and ITSN1) and they were coherent with the literature. Besides, we examined whether the main isoform of each gene -as predicted by APPRIS- was the most likely to have the annotated gene functions and it occurs in 99.4% of the genes. We also evaluated the predictions for isoform-specific functions provided by the CAFA3 challenge and results were also convincing. To make these results available to the scientific community, we have deployed a web application to consult ISOGO predictions (https://biotecnun.unav.es/app/isogo). Initial data, website link, isoform-specific GO function predictions and R code is available at https://gitlab.com/icassol/isogo.

The use of mixed collagen-Matrigel matrices of increasing complexity recapitulates the biphasic role of cell adhesion in cancer cell migration: ECM sensing, remodeling and forces at the leading edge of cancer invasion.

The migration of cancer cells is highly regulated by the biomechanical properties of their local microenvironment. Using 3D scaffolds of simple composition, several aspects of cancer cell mechanosensing (signal transduction, EMC remodeling, traction forces) have been separately analyzed in the context of cell migration. However, a combined study of these factors in 3D scaffolds that more closely resemble the complex microenvironment of the cancer ECM is still missing. Here, we present a comprehensive, quantitative analysis of the role of cell-ECM interactions in cancer cell migration within a highly physiological environment consisting of mixed Matrigel-collagen hydrogel scaffolds of increasing complexity that mimic the tumor microenvironment at the leading edge of cancer invasion. We quantitatively show that the presence of Matrigel increases hydrogel stiffness, which promotes ß1 integrin expression and metalloproteinase activity in H1299 lung cancer cells. Then, we show that ECM remodeling activity causes matrix alignment and compaction that favors higher tractions exerted by the cells. However, these traction forces do not linearly translate into increased motility due to a biphasic role of cell adhesions in cell migration: at low concentration Matrigel promotes migration-effective tractions exerted through a high number of small sized focal adhesions. However, at high Matrigel concentration, traction forces are exerted through fewer, but larger focal adhesions that favor attachment yielding lower cell motility.

Removal of Phenolic Compounds from Water Using Copper Ferrite Nanosphere Composites as Fenton Catalysts.

Copper ferrites containing Cu+ ions can be highly active heterogeneous Fenton catalysts due to synergic effects between Fe and Cu ions. Therefore, a method of copper ferrite nanosphere (CFNS) synthesis was selected that also permits the formation of cuprite, obtaining a CFNS composite that was subsequently calcined up to 400 °C. Composites were tested as Fenton catalysts in the mineralization of phenol (PHE), p-nitrophenol (PNP) and p-aminophenol (PAP). Catalysts were characterized by transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and magnetic measurements. Degradation of all phenols was practically complete at 95% total organic carbon (TOC) removal. Catalytic activity increased in the order PHE < PNP < PAP and decreased when the calcination temperature was raised; this order depended on the electronic effects of the substituents of phenols. The as-prepared CFNS showed the highest catalytic activity due to the presence of cubic copper ferrite and cuprite. The Cu+ surface concentration decreased after calcination at 200 °C, diminishing the catalytic activity. Cuprite alone showed a lower activity than the CFNS composite and the homogeneous Fenton reaction had almost no influence on its overall activity. CFNS activity decreased with its reutilization due to the disappearance of the cuprite phase. Degradation pathways are proposed for the phenols.

3-D Quantification of Filopodia in Motile Cancer Cells.

We present a 3D bioimage analysis workflow to quantitatively analyze single, actin-stained cells with filopodial protrusions of diverse structural and temporal attributes, such as number, length, thickness, level of branching, and lifetime, in time-lapse confocal microscopy image data. Our workflow makes use of convolutional neural networks trained using real as well as synthetic image data, to segment the cell volumes with highly heterogeneous fluorescence intensity levels and to detect individual filopodial protrusions, followed by a constrained nearest-neighbor tracking algorithm to obtain valuable information about the spatio-temporal evolution of individual filopodia. We validated the workflow using real and synthetic 3-D time-lapse sequences of lung adenocarcinoma cells of three morphologically distinct filopodial phenotypes and show that it achieves reliable segmentation and tracking performance, providing a robust, reproducible and less time-consuming alternative to manual analysis of the 3D+t image data.

Characterization of three-dimensional cancer cell migration in mixed collagen-Matrigel scaffolds using microfluidics and image analysis.

Microfluidic devices are becoming mainstream tools to recapitulate in vitro the behavior of cells and tissues. In this study, we use microfluidic devices filled with hydrogels of mixed collagen-Matrigel composition to study the migration of lung cancer cells under different cancer invasion microenvironments. We present the design of the microfluidic device, characterize the hydrogels morphologically and mechanically and use quantitative image analysis to measure the migration of H1299 lung adenocarcinoma cancer cells in different experimental conditions. Our results show the plasticity of lung cancer cell migration, which turns from mesenchymal in collagen only matrices, to lobopodial in collagen-Matrigel matrices that approximate the interface between a disrupted basement membrane and the underlying connective tissue. Our quantification of migration speed confirms a biphasic role of Matrigel. At low concentration, Matrigel facilitates migration, most probably by providing a supportive and growth factor retaining environment. At high concentration, Matrigel slows down migration, possibly due excessive attachment. Finally, we show that antibody-based integrin blockade promotes a change in migration phenotype from mesenchymal or lobopodial to amoeboid and analyze the effect of this change in migration dynamics, in regards to the structure of the matrix. In summary, we describe and characterize a robust microfluidic platform and a set of software tools that can be used to study lung cancer cell migration under different microenvironments and experimental conditions. This platform could be used in future studies, thus benefitting from the advantages introduced by microfluidic devices: precise control of the environment, excellent optical properties, parallelization for high throughput studies and efficient use of therapeutic drugs.

Characterization of the role of collagen network structure and composition in cancer cell migration.

The geometry of 3D collagen networks is a key factor that influences the behavior of live cells within extra-cellular matrices. This paper presents a method for automatic quantification of the 3D collagen network geometry with fiber resolution in confocal reflection microscopy images. The proposed method is based on a smoothing filter and binarization of the collagen network followed by a fiber reconstruction algorithm. The method is validated on 3D collagen gels with various collagen and Matrigel concentrations. The results reveal that Matrigel affects the collagen network geometry by decreasing the network pore size while preserving the fiber length and fiber persistence length. The influence of network composition and geometry, especially pore size, is preliminarily analyzed by quantifying the migration patterns of lung cancer cells within microfluidic devices filled with three different hydrogel types. The experiments reveal that Matrigel, while decreasing pore size, stimulates cell migration. Further studies on this relationship could be instrumental for the study of cancer metastasis and other biological processes involving cell migration.

Carbon xerogel microspheres and monoliths from resorcinol-formaldehyde mixtures with varying dilution ratios: preparation, surface characteristics, and electrochemical double-layer capacitances.

Carbon xerogels in the form of microspheres and monoliths were obtained from the sol-gel polymerization of resorcinol and formaldehyde in the presence of potassium carbonate as catalyst, using water as solvent and two different molar dilution ratios. The objectives of this study were as follows: to investigate the effect of the dilution ratio, polymerization reaction time, and temperature on the rheological properties of the sols used to prepare the carbon xerogel microspheres and monoliths; and to determine the influence of their preparation methods and shapes on their surface characteristics and electrochemical double-layer (EDL) capacitance. An increase in the molar dilution ratio produced a decrease in the apparent activation energy of the sol-gel transition. Carbon xerogel microspheres were steam-activated at different burnoff percentages. The morphology, surface area, porosity, and surface chemistry of samples were determined. The main difference between the carbon xerogel microspheres and monoliths was that the latter are largely mesoporous. Better electrochemical behavior was shown by carbon xerogels in monolith than in microsphere form, but higher gravimetric and volumetric capacitances were found in activated carbon xerogel microspheres than in carbon xerogel monoliths.

Growth and spontaneous differentiation of umbilical-cord stromal stem cells on activated carbon cloth.

We have investigated the capacity of activated carbon cloth to support the growth and differentiation of human mesenchymal umbilical-cord stromal stem cells. Our results demonstrate that this scaffold provides suitable conditions for the development of cell-derived matrix proteins and facilitates the growth of undifferentiated stem cells with the ability to induce osteogenic and chondrogenic differentiation. Immunoflourescence staining revealed extensive expression of collagen in all the samples, and collagen type II and osteopontin within the samples cultivated in specific differentiation-inducing media. Cell growth and the formation of natural collagen, calcium-magnesium carbonate and hydroxyapatite crystals, together with the self-assemblage of collagen to produce suprafibrillar arrangements of fibrils all occur simultaneously and can be studied together ex vivo under physiological conditions. Furthermore, the spontaneous differentiation of stem cells cultured on activated carbon cloth with no osteogenic supplements opens up new possibilities for bone-tumour engineering and treatment of traumatic and degenerative bone diseases.

Surgical management of liver hydatidosis: a multicentre series of 1412 patients.

BACKGROUND: The management of hydatid liver disease (HLD) includes various nonsurgical and surgical treatment options. METHODS: The purpose of the present longitudinal study was to report the changes in surgical management and the consequent outcome of HLD patients in 10 referral surgical centres in Argentina from 1975 to 2007. The study result analysis was divided into two study periods (1975-1990 and 1991-2007). RESULTS: A total of 1412 patients underwent radical (Group 1: 396 patients), conservative (Group 2: 748 patients) or combined (Group 3: 536 interventions in 268 patients) surgical procedures. The overall mortality and complication rate (Clavien I-IV) was 1.8 and 39% respectively. The complication rate was significantly lower in Group 1 (26%) compared with Group 2 (45%) and Group 3 (42%) There was a significant decrease in mortality (2.3 vs. 1%), complication (42 vs. 34%) and early reoperation (12 vs. 6%) rates between the first study part (918 patients) and the second study part (494 patients). During a median follow-up of 7 years, there was a significant decrease in the first part of this study in the late reoperation rate (8.4-3%) and in disease recurrence (9-1.6%). CONCLUSION: This large national observational multicentre series shows a significant improvement in surgical management of HLD in Argentina, with a decrease in mortality, morbidity, early and late reoperation and recurrence rates. A recent trend was observed in favour of an earlier diagnosis, less complicated clinical presentation and recent use of minimally invasive approaches.

Diagnóstico y tratamiento del cáncer periampular / Diagnosis and treatment of periampullar cancer

Antecedentes: Los tumores periampulares constituyen una unidad anatómica, embriológica y clínica permitiendo la aplicación de procedimientos diagnósticos y terapéuticos comunes. Objetivos: Este estudio ha sido diseñado para evaluar retrospectivamente: 1 - La incidencia de sintomatoloía clínica en relación a las distintas localizaciones. 2 - La utilización de los métodos diagnósticos. 3 - Análisis de la estadificación y tratamiento, según su localización y estadio. 4 - Análisis de los resultados del tratamiento quirúrgico resectivo, paliativo y el mini-invasivo. 5 - Incidencia de las variables histopatológicas (grado de diferenciación) como factores pronósticos de sobrevida. 6 - Estudio comparativo de la sobrevida corregida por estadio y método de tratamiento. 7 - Evaluación de la morbimortalidad observada en nuestra serie. 8 - Efectuar una actualización bibliográfica del tema. Lugar de aplicación: Los pacientes fueron estudiados y tratados en dos centros hospitalarios universitarios de referencia de la ciudad de La Plata y en práctica privada. Diseño: Estudio retrospectivo observacional. Población: 460 pacientes tratados entre 1990 y 2005. Métodos: 252 pacientes pertenecían al sexo masculino, con una media etárea de 55.8 años, con un rango entre 34 - 83 años. La localización topográfica fue de 283 en páncreas, 113 en la ampolla de Vater, 56 en vía biliar distal y 8 en duodeno...

Surface area and microporosity of carbon aerogels from gas adsorption and small- and wide-angle X-ray scattering measurements.

A carbon aerogel was obtained by carbonization of an organic aerogel prepared by sol-gel polymerization of resorcinol and formaldehyde in water. The carbon aerogel was then CO(2) activated at 800 degrees C to increase its surface area and widen its microporosity. Evolution of these parameters was followed by gas adsorption and small- and wide-angle X-ray scattering (SAXS and WAXS, respectively) with contrast variation by using dry and wet (immersion in benzene and m-xylene) samples. For the original carbon aerogel, the surface area, S(SAXS), obtained by SAXS, is larger than that obtained by gas adsorption (S(ads)). The values become nearly the same as the degree of activation of the carbon aerogel increases. This feature is due to the widening of the narrow microporosity in the carbon aerogel as the degree of activation is increased. In addition, WAXS results show that the short-range spatial correlations into the assemblies of hydrocarbon molecules confined inside the micropores are different from those existing in the liquid phase.

The impact of selective logging and forest conversion for subsistence agriculture and pastures on terrestrial nutrient dynamics in the Amazon

The conversion of primary forests in the Amazon via selective logging, slash and burn agriculture, and pasture establishment, will continue because of the increasing demand for timber and agricultural land. Forest conversion has major impacts on the stocks and flows of essential plant nurtrients. For example, the burning of slashed vegetation results in most of the carbon and nutrients in the biomass being volatilized during burning. Nutrient stocks are further depleted by the nutrient exports in timber and crop harvests. Poor crop and pasture mamagement practices can result in rapid declines in soil fertility and reduced vegetation regrowth potential. These changes can influence the rate of secondary forest regrowth and carbon sequestration on abandoned crop and pasture lands. The dominant land use practives following forest conversion in the Amazon are identified and the data on the impact of selective logging, subsistence cropping, and extensive pastures, on nutrient stocks and budgets in terrestrial Amazonian ecosystems are reviewed.

Pseudoquistes pancreáticos postnecróticos / Pancretic pseudocyst postnecrotic

Considerando múltiples factores que influyen en el proceso evolutivo de los pseudoquistes pancreáticos postnecróticos se efectúa un análisis sobre 34 pacientes asistidos en 3 centros quirúrgicos de nuestra ciudad en el término de 10 años, estableciéndose las distintas alternativas terapéuticas en función de los mismos.

Restitución del flujo bilioentérico mediante el asa de Hivet-Warren-Praderi: nuestra experiencia / Biliary-enteric flux restitution the Hivet-Warren-Praderi loop: our experience

Se presenta la experiencia con el uso del asa de Hivet-Warren_Praderi en las derivaciones biliodigestivas: se enfatiza los beneficios que dicha asa proporciona como ser rapidez, simplicidad y seguridad, siendo su valor funcional idéntico al asa en Y de Roux. Se resumen las ventajas, técnica e indicaciones para su uso. Se concluye que es un método recomendable y de elección en casos de derivaciones biliodigestivas. Los resultados precedentemente mencionados se basan en 72 pacientes operados.

Valoración de la esfinteropapilotomia endoscopica (EPE) mediante radiocolangiodebitometria operatoria (RCDM)

Con resultados iniciales de un estudio prospectivo, 5 pacientes con descompresión mediante EPE y posterior cirugía a cielo abierto complementaria son evaluados por RCDM seriada, con débito x = 18.6 cc/minuto ñ 2.3 (V.N. > ou =), el análisis comparativo con 24 EPDT amplios a cielo abierto demuestra comportamientos debitométricos similares (x = 18.3 ñ 2.0 cc/minuto). Se realizan algunas consideraçciones fisiopatológicas de acuerdo a las curvas evolutivas promedio, a verificar con muestras más amplias