Inferring the clonal identity of single cells from RNA-seq data with Unique Molecular Identifiers

Cancer is an evolutionary disease, in which heterogeneous populations of tumor cells can emerge, proliferate, and disappear depending on selective and neutral processes. This principle has been observed in many studies of acute myeloid leukemia (AML), which is the most common blood cancer in adults. Clonal heterogeneity and evolution have been proposed to play a role in the high relapse rate of this type of cancer. In order to understand this feature, it is crucial to have adequate clinical and experimental models that can provide enough data to elucidate the evolutionary history of a tumor, such as patient-derived xenografts (PDX). These models can be combined with high-resolution sequencing technologies, such as single-cell RNA-seq, to provide a detailed view of the heterogeneity and molecular features of the tumor. However, adequate analytical tools have to be applied and developed in order to fully exploit such datasets. Here I present the analysis of the clonal heterogeneity of an AML patient and the corresponding PDX model, which was treated with multiple rounds of chemotherapy. This model allowed to study the response of the tumor populations to the pressure induced by the therapy, and the possible evolutionary forces behind it. Datasets for these AML samples were generated with multiple types of sequencing methods, one of which was single-cell RNA sequencing. To enable the analysis of somatic mutations and clonal populations in this kind of data, I developed a software package, which is capable of extracting and proofreading variant sequences by making use of Unique Molecular Identifiers (UMIs), which are sequence barcodes that allow to distinguish reads that come from PCR amplification duplicates. The benefits of employing this proofreading approach for variant calling and for inferring the clonal identity of single cells were demonstrated. Finally, I applied to the analysis of the single-cell data of the AML PDX samples that were treated with chemotherapy, as well as other datasets with UMI-based sequencing

¿Políticas para la economía del futuro? La economía colaborativa y las plataformas digitales en el Perú: un análisis de la respuesta del Congreso de la República (2014-2019)

En los últimos cuatro años, las plataformas digitales en diversos sectores han ingresado al mercado peruano, siendo en los sectores de transporte y reparto a domicilio donde han ganado mayor presencia, logrando así posicionarse entre los ciudadanos. En una ciudad como Lima donde no se cuenta con un sistema de transporte integrado y eficiente, los ciudadanos gastan muchas horas en movilizarse. Por ello, buscan nuevas estrategias para disminuir dicho tiempo y los taxis por aplicación parecen ser parte de la respuesta. Asimismo, una manera de generar trabajo y facilitar las transacciones entre los ciudadanos, se da a través de las aplicaciones de reparto a domicilio pues, estas recogen y entregan desde un documento, una hamburguesa del restaurante de moda hasta las medicinas recetadas por el doctor. No obstante, el surgimiento de las plataformas digitales en el contexto actual, donde prima el neoliberalismo, invita a reflexionar las consecuencias que se generan, el futuro del trabajo dentro de la cuarta revolución tecnológica y el papel que debe asumir el Estado. La presente investigación se pregunta por cómo se configura la respuesta del Estado a la necesidad de regulación de las plataformas digitales en los últimos cuatro años, a partir del análisis de las iniciativas legislativas tomadas por tres congresistas de diferentes grupos parlamentarios dentro del Congreso de la República. La hipótesis que se demuestra en esta investigación es que los factores que configuraron las respuestas de los congresistas de tres grupos parlamentarios distintos frente a la regulación de las plataformas digitales son: la presencia y características de los eventos de enfoque que pusieron la atención sobre estas plataformas, las características de los emprendedores de políticas que la impulsan (los congresistas) entendidas en términos de ideologías , incentivos y/o motivaciones políticas o personales que los impulsan a actuar y la forma como entienden el papel de la economía colaborativa, concretamente en el caso de las plataformas digitales objeto de este estudio Uber taxi y Glovo.Tesi

Anti-atherogenic properties associated with the antioxidant activity from the hydrophilic extracts of Halimeda incrassata (Chlorophyta, Bryopsidales)

Seaweeds are a source of natural antioxidants having potential application in oxidative stress and associated diseases. In this work, anti-atherogenic properties associated with the antioxidant activity from the hydrophilic extracts of Halimeda incrassata were studied. The phenolic content assessed inthe aqueous extract and fraction phenolic acids (FPA) was 0.13 ± 0.05 and 0.47 ± 0.09 mg of gallic acid equivalents (GAE)/g dry seaweed, respectively. In DPPH?, radical scavenging assay fractions exhibited a dependent concentration. The seaweeds extract inhibited the desoxirribose oxidation in the presenceor absence of EDTA (IC50 = 1.91± 0.09 mg/mL) (IC50 = 2.95 ± 0.01 mg/mL). In vivo antioxidant properties of FPA-H.incrassata were investigated in rats with a CCl4-induced liver injury. Pre-treatment with H.incrassata led to approximately 50% reductions in liver TBARS levels. The treatment with H. incrassataFPA also increased the activity of the CAT enzyme, which in turn resulted in an enhanced antioxidantdefense. The expression of Catalase by PCR-RT technique demonstrated a higher gene expression when compared with that which was observed in the CCl 4-treated group. Antiatherogenic properties were studied in the inhibition of lipoprotein oxidation mediated by Cu2+ or HRP/H2O2, free radicalscavenging, and metal ion chelation, and it was dose dependent with a higher concentration needed for the aqueous extract than for the FPA fraction. Antioxidant activity was also improved in macrophages as evaluated in the cell supernatant (by TBARS formation); and by luminol enhanced chemiluminescence after cell activation with zymosan; and a degree of cell lipoperoxidation wasdecreased by the Halimeda incrassata extract. The results of this work add to the antioxidant potential of the seaweed for its application in oxidative stress associated conditions.Fil: Vidal-Novoa, Alexis. Universidad de la Habana. Facultad de Biología; CubaFil: Costa-Mugica, Ariadna. Universidad de la Habana. Facultad de Biología; CubaFil: Zulueta Díaz, Yenisleidy de Las Mercedes. Universidad de la Habana. Facultad de Biología; Cuba. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Investigaciones en Química Biológica de Córdoba; ArgentinaFil: Diaz-Gutierrez, Daylín. Universidad de la Habana. Facultad de Biología; CubaFil: de Oliveira e Silva, Ana, Mara. Universidade de Sao Paulo; BrasilFil: Vazquez, Ana María. Center For Molecular Inmunology; CubaFil: Claudina, Zaldívar-Munoz. Universidad de la Habana. Facultad de Biología; CubaFil: Dalva, Assuncao Portari de Mancini. Institute Butantan Sao Paulo; BrasilFil: Mancini-Filho, Jorge. Universidade de Sao Paulo; Brasi

Aprendizaje socioemocional en tiempos virtuales, una mirada sobre la ansiedad y otros problemas emocionales desde estrategias didácticas modernas

El presente proyecto de investigación se centra en la ansiedad abordada a través del aprendizaje socioemocional y los ambientes virtuales de aprendizaje. Con el objetivo de comprender las bases teóricas y los resultados obtenidos al utilizar herramientas que puedan ser usadas on line y off line, por ejemplo, classroom, kahoot, edpuzzle, slides o pdf, empleadas por algunos docentes de Univirtual e Ilex para un mejor desarrollo académico, en particular después de la pandemia del COVID-19 la cual provocó una adopción masiva de tecnologías de la información y la comunicación (TIC) en el sistema educativo. El estudio se llevó a cabo en la Universidad Tecnológica de Pereira en el periodo 2022-2 con la participación de un grupo de docentes y de estudiantes de Ilex en los cursos cuatro (4) y cinco (5), también estudiantes de Univirtual de la licenciatura en Tecnología con énfasis en Informática Educativa de la facultad de Educación de la UTP, para ello se empleó una metodología cualitativa que incluye la realización de entrevistas abiertas a los docentes con el objetivo de recopilar sus experiencias en el contexto de la enseñanza a través de ambientes virtuales de aprendizaje. Se utilizó la entrevista codificada para recopilar la información de los estudiantes y su proceso en las clases. La información recopilada se analizó mediante un sistema de comparación entre los datos obtenidos de las entrevistas y la teoría, lo que permitió obtener conclusiones y plantear recomendaciones para proyectos futuros. Tales como la identificación de algunas falencias emocionales, en particular la ansiedad y el estrés causadas por un uso precario de herramientas TIC, que en cambio pueden ser útiles a la hora de querer un mejoramiento significativo en las clases virtuales. El enfoque cualitativo del estudio proporcionó una comprensión más profunda de las implicaciones de la ansiedad en el aprendizaje socioemocional y los ambientes virtuales de aprendizaje.This research project focuses on anxiety addressed through social-emotional learning and virtual learning environments. With the aim of understanding the theoretical bases and the results obtained by using tools that can be used online and offline, for example, classroom, kahoot, edpuzzle, slides or pdf, used by some teachers of Univirtual and Ilex for a better academic development, particularly after the pandemic of COVID-19 which caused a massive adoption of information and communication technologies (ICT) in the educational system. The study was carried out at the Technological University of Pereira with the participation of a group of teachers and students, using a qualitative methodology that includes conducting open interviews with teachers in order to collect their experiences in the context of teaching through virtual learning environments. The coded interview was also used to collect information from the students and their process in the classes. The information collected was analyzed through a system of comparison between the data obtained from the interviews and the theory, which allowed conclusions to be drawn and recommendations for future projects to be put forward. The qualitative approach of the study provided a deeper understanding of the implications of anxiety in socioemotional learning and virtual learning environments.PregradoLicenciado(a) en Comunicación e Informática EducativaTabla de contenidos Resumen.......................................................................................................................... 7 Abtract............................................................................................................................. 9 Introducción .................................................................................................................. 10 Capítulo 1. Ansiedad, aprendizaje socioemocional y AVAS......................................... 15 La ansiedad: .................................................................................................................. 17 Ambientes virtuales de aprendizaje: ............................................................................. 26 Capítulo 2: Construcción metodológica de las fases en el contexto virtual educativo Utp............................................................................................................................................. 31 Método hipotético-deductivo:....................................................................................... 31 Enfoque: Cualitativo (socio-constructivista) ................................................................ 35 Tipo de estudio: Exploratorio ....................................................................................... 37 Proceso para realizar una investigación exploratoria.................................................... 40 2.Contexto de la investigación. “Aprendizaje socioemocional en tiempos virtuales, una mirada sobre la ansiedad y otros problemas emocionales desde estrategias didácticas modernas.” ................................................................................................................................ 41 3. POBLACIÓN............................................................................................................ 46 4.Instrumentos............................................................................................................... 49 Capítulo 3: Análisis y resultados sobre los métodos del aprendizaje socioemocional en ambientes virtuales de aprendizaje como estrategias para identificar problemas emocionales dentro de la educación virtual universitaria. ............................................................................. 53 Análisis de la información: ........................................................................................... 79 Conclusiones:................................................................................................................ 83 Recomendaciones: ........................................................................................................ 90 Referencias bibliográficas:............................................................................................ 9

Blood component requirements in liver transplantation: effect of 2 thromboelastometry-guided strategies for bolus fibrinogen infusion, the TROMBOFIB randomized trial

Background: A low plasma fibrinogen level influences blood component transfusion. Thromboelastometry provides clinical guidance for fibrinogen replacement in liver transplantation (LT). Objectives: We hypothesized that infusions of fibrinogen concentrate to reach an A10FIBTEM value of 11 mm during LT could reduce red blood cell (RBC) and other component and fluid requirements in comparison to standard care. Methods: This randomized, blinded, multicenter trial in 3 hospitals enrolled 189 LTscheduled patients allocated to an intervention target (A10FIBTEM, 11 mm) or a standard target (A10FIBTEM, 8 mm); 176 patients underwent LT with fibrinogen replacement. Data were analyzed by intention-to-treat (intervention group, 91; control group, 85). Blood was extracted, and fibrinogen kits were prepared to bring each patient's fibrinogen level to the assigned target at the start of LT, after portal vein clamping, and after graft reperfusion. The main outcome was the proportion of patients requiring RBC transfusion during LT or within 24 hours. Results: The proportion of patients requiring RBCs did not differ between the groups: intervention, 74.7% (95% CI, 65.5%-83.3%); control, 72.9% (95% CI, 62.2%-82.0%); absolute difference, 1.8% (95% CI, −11.1% to 14.78%) (P = .922). Thrombotic events occurred in 4% of the patients in both groups; reoperation and retransplantation rates and mortality did not differ. Nearly 70% of the patients in both groups required fibrinogen concentrate to reach the target. Using an 11-mm A10FIBTEM target increased the maximum clot firmness without affecting safety. However, this change provided no clinical benefits. Conclusion: The similar low plasma fibrinogen concentrations could explain the lack of significant between-group outcomes

Allogeneic Hematopoietic Stem Cell Transplantation in Transformed Follicular Lymphoma (tFL): Results of a Retrospective Multicenter Study from GELTAMO/GETH-TC Spanish Groups

Simple Summary Follicular lymphoma (FL) is the most prevalent subtype of indolent lymphoma, accounting for 70% of all cases. The estimated risk of histological transformation (tFL), such as diffuse large B cell lymphoma (DLBCL), varies from 2-3% per year to 7-8% at 10 years in different series. Treatment after transformation is not clearly established. Allogeneic hematopoietic stem cell transplantation (alloSCT) could be an option for these patients, but it has not been widely explored. We analyze the efficacy and toxicity of alloSCT in 43 patients from 14 Spanish centers. We observed long-term survival in around one third of the patients, especially those who developed chronic graft versus host disease, indicating that alloSCT continues to be a potentially curative option for patients with tFL, mainly due to the graft versus lymphoma effect. Background: Transformation of follicular lymphoma into an aggressive lymphoma (tFL) worsens the prognosis and the standard treatment is not completely defined. Allogeneic hematopoietic stem cell transplantation (alloSCT) could be a potentially curative option for these patients, but it has not been widely explored. Methods: We designed a retrospective multicenter study to analyze the efficacy and toxicity of alloSCT in tFL patients and potential prognostic factors of survival. Results: A total of 43 patients diagnosed with tFL who underwent alloSCT in 14 Spanish centers between January 2000 and January 2019 were included. Median age was 44 (31-67) years. After a median follow-up of 58 months, estimated 5-year overall survival (OS) and progression-free survival (PFS) were both 35%. Estimated 100-day and 1-year non-relapse mortality (NRM) were 20% and 34%, respectively. The type of conditioning regimen (3-year OS of 52% vs. 20%, respectively, for reduced-intensity vs. myeloablative conditioning) and development of chronic graft versus host disease (cGVHD) (3-year OS of 75% vs. 40%) were the only factors significantly associated with OS. The only variable with an independent association with OS was cGVHD (HR, 3.4; 95% CI, 1.2-9.6). Conclusions: Our results indicate that alloSCT continues to be a potentially curative option for patients with tFL

Allogeneic Stem Cell Transplantation in Mantle Cell Lymphoma; Insights into Its Potential Role in the Era of New Immunotherapeutic and Targeted Therapies: The GETH/GELTAMO Experience

Allo-SCT is a curative option for selected patients with relapsed/refractory (R/R) MCL, but with significant NRM. We present the long-term results of patients receiving allo-SCT in Spain from March 1995 to February 2020. The primary endpoints were EFS, OS, and cumulative incidence (CI) of NRM, relapse, and GVHD. We included 135 patients, most (85%) receiving RIC. After a median follow-up of 68 months, 5-year EFS and OS were 47 and 50%, respectively. Overall and CR rates were 86 and 80%. The CI of relapse at 1 and 3 years were 7 and 12%. NRM at day 100 and 1 year were 17 and 32%. Previous ASCT and Grade 3-4 aGVHD were associated with a higher NRM. Grade 3-4 aGVHD, donor type (mismatch non-related), and the time-period 2006-2020 were independently related to worse EFS. Patients from 1995-2005 were younger, most from HLA-identical sibling donors, and were pretreated less. Our data confirmed that allo-SCT may be a curative option in R/R MCL with low a CI of relapse, although NRM is still high, being mainly secondary to aGVHD. The arrival of new, highly effective and low toxic immunotherapeutic or targeted therapies inevitably will relegate allo-SCT to those fit patients who fail these therapies, far away from the optimal timing of treatment

Allogeneic Stem Cell Transplantation in Mature T Cell and Natural Killer/T Neoplasias: A Registry Study from Spanish GETH/GELTAMO Centers

Despite advances in understanding the biology of mature T and natural killer (NK)/T cell neoplasia, current therapies, even the most innovative ones, are still far from ensuring its cure. The only treatment to date that has been shown to control aggressive T cell neoplasms in the long term is allogeneic stem cell transplantation (alloSCT). We aim to report the results of alloSCT for advanced mature T and NK/T neoplasias performed in centers from our national GELTAMO/GETH (Grupo Español de Linfoma y Trasplante de Médula Ósea/Grupo Español de Trasplante Hematopoyético y Terapia Celular) over the past 25 years. As a secondary objective, we analyzed the results of alloSCT from haploidentical donors. We performed a retrospective analysis of all patients who received an alloSCT in Spanish centers (n = 201) from September 1995 to August 2018. The 2-year overall survival (OS) and disease-free survival (DFS) were 65.5% and 58.2%, respectively. The univariate for OS and DFS showed statistically different hazard ratios for conditioning intensity, response pre-alloSCT, comorbidity index, donor/receptor cytomegalovirus status and Eastern Cooperative Oncology Group (ECOG) pre-alloSCT, but only a better ECOG pre-alloSCT remained significant in the multivariate analysis. There was an increased incidence of relapse in those patients who did not develop chronic graft-versus-host disease (GVHD) and an increased risk of death in those developing moderate to severe acute GVHD. The 1-year nonrelapse mortality was 21.9% and was mainly due to GVHD (30%) and bacterial infections (17%). When comparing unrelated donors with haploidentical donors, we found similar results in terms of OS and DFS. There was, however, a reduction of acute GVHD in the haploidentical group (P = .04) and trend to a reduction of chronic GVHD. In conclusion, alloSCT is the only curative option for most aggressive T cell neoplasias. Haploidentical donors offer similar results to related donors in terms of survival with a reduction of acute GVHD

Prevalence of submicroscopic malaria infection in immigrants living in Spain

BACKGROUND: The importance of submicroscopic malaria infections in high-transmission areas could contribute to maintain the parasite cycle. Regarding non-endemic areas, its importance remains barely understood because parasitaemia in these afebrile patients is usually below the detection limits for microscopy, hence molecular techniques are often needed for its diagnosis. In addition to this, the lack of standardized protocols for the screening of submicroscopic malaria in immigrants from endemic areas may underestimate the infection with Plasmodium spp. The aim of this study was to assess the prevalence of submicroscopic malaria in afebrile immigrants living in a non-endemic area. METHODS: A prospective, observational, multicentre study was conducted. Afebrile immigrants were included, microscopic observation of Giemsa-stained thin and thick blood smears, and two different molecular techniques detecting Plasmodium spp. were performed. Patients with submicroscopic malaria were defined as patients with negative blood smears and detection of DNA of Plasmodium spp. with one or both molecular techniques. Demographic, clinical, analytical and microbiological features were recorded and univariate analysis by subgroups was carried out with STATA v15. RESULTS: A total of 244 afebrile immigrants were included in the study. Of them, 14 had a submicroscopic malaria infection, yielding a prevalence of 5.7% (95% confidence interval 3.45-9.40). In 71.4% of the positive PCR/negative microscopy cases, Plasmodium falciparum alone was the main detected species (10 out of the 14 patients) and in 4 cases (28.6%) Plasmodium vivax or Plasmodium ovale were detected. One patient had a mixed infection including three different species. CONCLUSIONS: The prevalence of submicroscopic malaria in afebrile immigrants was similar to that previously described in Spain. Plasmodium vivax and P. ovale were detected in almost a third of the submicroscopic infections. Screening protocols for afebrile immigrants with molecular techniques could be useful for a proper management of these patients.This work was funded by projects PI14/01671, PI17/01791 and PI14CIII/00014, from the Instituto de Salud Carlos III (Ministry of Economy, Industry and Competitiveness) and cofounded by the European Regional Development Fund, and approved by the Ethics Committee of our Institution. There was no funding from the PCR manufacturers; they did not play any role in data analysis or in the reporting of the results.S

Multifaceted regulation of hepatic lipid metabolism by YY1

Recent studies suggested that dysregulated YY1 plays a pivotal role in many liver diseases. To obtain a detailed view of genes and pathways regulated by YY1 in the liver, we carried out RNA sequencing in HepG2 cells after YY1 knockdown. A rigid set of 2,081 differentially expressed genes was identified by comparing the YY1-knockdown samples (n = 8) with the control samples (n = 14). YY1 knockdown significantly decreased the expression of several key transcription factors and their coactivators in lipid metabolism. This is illustrated by YY1 regulating PPARA expression through binding to its promoter and enhancer regions. Our study further suggest that down-regulation of the key transcription factors together with YY1 knockdown significantly decreased the cooperation between YY1 and these transcription factors at various regulatory regions, which are important in regulating the expression of genes in hepatic lipid metabolism. This was supported by the finding that the expression of SCD and ELOVL6, encoding key enzymes in lipogenesis, were regulated by the cooperation between YY1 and PPARA/RXRA complex over their promoters