2D and 3D Shape Descriptors

The field of computer vision studies the computational tools and methods required for computers to be able to process visual information, for example images and video. Shape descriptors are one of the tools commonly used in image processing applications. Shape descriptors are mathematical functions which are applied to an image and produce numerical values which are representative of a particular characteristic of the image. These numerical values can then be processed in order to provide some information about the image. For example, these values can be fed to a classifier in order to assign a class label to the image. There are a number of shape descriptors already existing in the literature for 2D and 3D images. The aim of this thesis is to develop additional shape descriptors which provide an improvement over (or an alternative to) those already existing in the literature. A large majority of the existing 2D shape descriptors use surface information to produce a measure. However, in some applications surface information is not present and only partially extracted contours are available. In such cases, boundary based shape descriptors must be used. A new boundary based shape descriptor called Linearity is introduced. This measure can be applied to open or closed curve segments. In general the availability of 3D images is comparatively smaller than that of 2D images. As a consequence, the number of existing 3D shape descriptors is also relatively smaller. However, there is an increasing interest in the development of 3D descriptors. In this thesis we present two basic 3D measures which afterwards are modified to produce a range of new shape descriptors. All of these descriptors are similar in their behaviour, however they can be combined and applied in different image processing applications such as image retrieval and classification. This simple fact is demonstrated through several examples.Mexican Science Council (Consejo Nacional de Ciencia y Tecnologia, CONACyT

Video tracking of dairy cows for assessing mobility scores

Lameness afflicts a large proportion of dairy herds, but could be considerably reduced by automated monitoring by CCTV. Key to this is reliable, robust detection and tracking of individual cows in crowded video sequences. We introduce a novel detection and tracking method, based on the Viola-Jones detector. We show that animals can be tracked and their overall gait patterns and speed automatically extracted from video sequences. Preliminary work on identification of individual animals through principal component analysis and SIFT feature matching is also described

Remodeling of the m6A RNA landscape in the conversion of acute lymphoblastic leukemia cells to macrophages

We thank CERCA Programme/Generalitat de Catalunya for institutional support. This work was supported by the Health Department PERIS-project no. SLT/002/16/00374 and AGAUR-projects no. 2017SGR1080 of the Catalan Government (Generalitat de Catalunya); Ministerio de Ciencia e Innovación (MCI), Agencia Estatal de Investigación (AEI) and European Regional Development Fund (ERDF) project no. RTI2018-094049-B-I00; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 743168); the Varda and Boaz Dotan Research Center in Hemato-oncology affiliated to the Tel Aviv University; the Cellex Foundation; and “la Caixa” Banking Foundation (LCF/PR/GN18/51140001). ME is an ICREA Research Professor.Peer Reviewed"Article signat per 12 autors/es: Alberto Bueno-Costa, David Piñeyro, Carlos A. García-Prieto, Vanessa Ortiz-Barahona, Laura Martinez-Verbo, Natalie A. Webster, Byron Andrews, Nitzan Kol, Chen Avrahami, Sharon Moshitch-Moshkovitz, Gideon Rechavi & Manel Esteller"Postprint (published version

Towards sustainable training in essential computing research skills in the Netherlands

Life science research increasingly depends on computational skills that enable efficient work with large complex datasets. Unfortunately, formal curricula often lack training in this area. There is a need for specialised training that includes topics like shell scripting, basic programming skills in R or Python, data handling, reproducible computational research and open science

Reconstructing the Population Genetic History of the Caribbean

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean.Comment: 26 pages, 6 figures, and supporting informatio

Intervención de urbanismo táctico para la implementación de cruces seguros

A lo largo de este reporte se informa sobre las distintas labores, investigaciones y visitas de campo que se llevan a cabo en el Proyecto de Aplicación Profesional de Movilidad en el periodo de primavera 2021. Durante el cual se abordó la problemática de movilidad urbana y falta de infraestructura que cotidianamente experimentan los usuarios que atraviesan el cruce de Av. Ramón Corona, Colegiales, Libertad y C. Degollado, denominado “Área de intervención”, ubicado en la colonia Mexicaltzingo, Guadalajara, Jal. La confluencia de diferentes dinámicas de las unidades transporte público colectivo en la zona, así como la falta de regulación y organización de las mismas generan un evidente desorden en materia de movilidad en el cruce de las calles anteriormente mencionadas, dicha problemática sumada a la ausencia infraestructura y señalética urbana adecuada que dote de claridad al espacio, pone en riesgo la vida de miles de usuarios que hacen uso del mismo diariamente, especialmente al peatón ya que la complejidad de la intersección de varias vialidades sumado a las falta de claridad en el espacio y los movimientos de transporte motorizado generan cruces inseguros entre vialidades que exponen al peatón. El objetivo principal de este trabajo es generar una intervención de urbanismo táctico así como una propuesta formal de implementación de cruces seguros en la intersección anteriormente mencionada, esto con la finalidad de organizar los movimientos peatonales en vialidades del área de intervención. La propuesta desarrollada podrá servir como un incentivo para que las autoridades correspondientes intervengan y ejecuten un proyecto de urbanismo permanente en base a la intervención de urbanismo táctico y la propuesta formal generada como resultado de este proyecto. Utilizamos una metodología de investigación mixta, por un lado utilizamos un abordaje cuantitativo para observar elementos medibles en el espacio, mientras que el abordaje cualitativo fue útil para obtener información acerca de la calidad del mismo.ITESO, A.C

A genome-wide association study follow-up suggests a possible role for PPARG in systemic sclerosis susceptibility

Introduction: A recent genome-wide association study (GWAS) comprising a French cohort of systemic sclerosis (SSc) reported several non-HLA single-nucleotide polymorphisms (SNPs) showing a nominal association in the discovery phase. We aimed to identify previously overlooked susceptibility variants by using a follow-up strategy.<p></p> Methods: Sixty-six non-HLA SNPs showing a P value <10-4 in the discovery phase of the French SSc GWAS were analyzed in the first step of this study, performing a meta-analysis that combined data from the two published SSc GWASs. A total of 2,921 SSc patients and 6,963 healthy controls were included in this first phase. Two SNPs, PPARG rs310746 and CHRNA9 rs6832151, were selected for genotyping in the replication cohort (1,068 SSc patients and 6,762 healthy controls) based on the results of the first step. Genotyping was performed by using TaqMan SNP genotyping assays. Results: We observed nominal associations for both PPARG rs310746 (PMH = 1.90 × 10-6, OR, 1.28) and CHRNA9 rs6832151 (PMH = 4.30 × 10-6, OR, 1.17) genetic variants with SSc in the first step of our study. In the replication phase, we observed a trend of association for PPARG rs310746 (P value = 0.066; OR, 1.17). The combined overall Mantel-Haenszel meta-analysis of all the cohorts included in the present study revealed that PPARG rs310746 remained associated with SSc with a nominal non-genome-wide significant P value (PMH = 5.00 × 10-7; OR, 1.25). No evidence of association was observed for CHRNA9 rs6832151 either in the replication phase or in the overall pooled analysis.<p></p> Conclusion: Our results suggest a role of PPARG gene in the development of SSc

Respiratory viruses detected in Mexican children younger than 5 years old with community-acquired pneumonia: a national multicenter study

Background: Acute respiratory infections are the leading cause of mortality in children worldwide, especially in developing countries. Pneumonia accounts for 16% of all deaths of children under 5 years of age and was the cause of death of 935 000 children in 2015. Despite its frequency and severity, information regarding its etiology is limited. The aim of this study was to identify respiratory viruses associated with community-acquired pneumonia (CAP) in children younger than 5 years old. Methods: One thousand four hundred and four children younger than 5 years of age with a clinical and/or radiological diagnosis of CAP in 11 hospitals in Mexico were included. Nasal washes were collected, placed in viral medium, and frozen at �70 C until processing. The first 832 samples were processed using the multiplex Bio-Plex/Luminex system and the remaining 572 samples using the Anyplex multiplex RT-PCR. Clinical data regarding diagnosis, clinical signs and symptoms, radiographic pattern, and risk factors were obtained and recorded. Results: Of the samples tested, 81.6% were positive for viruses. Respiratory syncytial virus (types A and B) was found in 23.7%, human enterovirus/rhinovirus in 16.6%, metapneumovirus in 5.7%, parainfluenza virus (types 1–4) in 5.5%, influenza virus (types A and B) in 3.6%, adenovirus in 2.2%, coronavirus (NL63, OC43, 229E, and HKU1) in 2.2%, and bocavirus in 0.4%. Co-infection with two or more viruses was present in 22.1%; 18.4% of the samples were negative. Using biomass for cooking, daycare attendance, absence of breastfeeding, and co-infections were found to be statistically significant risk factors for the presence of severe pneumonia. Conclusions: Respiratory syncytial virus (types A and B), human enterovirus/rhinovirus, and metapneumovirus were the respiratory viruses identified most frequently in children younger than 5 years old with CAP. Co-infection was present in an important proportion of the children

Rheumatoid arthritis and the role of oral bacteria

Rheumatoid arthritis (RA) and periodontal disease (PD) have shown similar physiopathologic mechanisms such as chronic inflammation with adjacent bone resorption in an immunogenetically susceptible host; however, PD has a well-recognized bacterial etiology while the cause of RA is unclear. Some reports have indicated that an infectious agent in a susceptible host could be one possible trigger factor for RA, and it has been suggested that oral microorganisms, specialty periodontal bacteria could be the infectious agent (mainly Porphyromonas gingivalis). It has been reported that PD is more frequent and more severe in patients with RA, suggesting a positive association between both diseases. There have been reports regarding the detection of antibodies against periodontal bacteria while other studies have identified periodontal bacterial DNA in serum and synovial fluid of RA patients and have explored the possible pathways of transport of periodontal bacterial DNA. In conclusion, there is no question that RA and PD have pathologic features in common and there is strong evidence of an association between both diseases, but further studies, including experimental models, are needed to demonstrate the arthritogenicity of oral microorganisms

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets