Detection of People Positive to COVID-19 through ATR-FTIR Spectra Analysis of Saliva using Machine Learning / Detección de Personas Positivas a COVID-19 mediante el Análisis de Espectros ATR-FTIR de Muestras de Saliva empleando Machine Learning

ABSTRACT COVID-19 is an infectious disease caused by the SARS-CoV-2 virus. This virus's spread is mainly through droplets released from the nose or mouth of an infected person. Although vaccines have been developed that effectively reduce the effects that this viral infection causes, the most effective method to contain the virus's spread is numerous tests to detect and isolate possible carriers. However, the response time, combined with the cost of actual tests, makes this option impractical. Herein, we compare some machine learning methodologies to propose a reliable strategy to detect people positive to COVID-19, analyzing saliva spectra obtained by Fourier transform infrared (FTIR) spectroscopy. After analyzing 1275 spectra, with 7 strategies commonly used in machine learning, we concluded that a multivariate linear regression model (MLMR) turns out to be the best option to identify possible infected persons. According to our results, the displacement observed in the region of the amide I of the spectrum, is fundamental and reliable to establish a border from the change in slope that causes this displacement that allows us to characterize the carriers of the virus. Being more agile and cheaper than reverse transcriptase polymerase chain reaction (RT-PCR), it could be reliably applied as a preliminary strategy to RT-PCR.

RESUMEN La COVID-19 es una enfermedad infecciosa ocasionada por el virus SARS-CoV-2. La propagación de este virus se produce principalmente a través de gotitas liberadas por la nariz o la boca de una persona infectada. Aunque se han desarrollado vacunas que permiten reducir efectivamente los efectos que esta infección viral provoca, el método más eficaz para contener la propagación del virus son las numerosas pruebas para detectar y aislar los posibles portadores. Sin embargo, el tiempo de respuesta, combinado con el costo de las pruebas reales, hace que esta opción sea poco práctica. Aquí, comparamos algunas metodologías de machine learning para proponer una estrategia confiable para detectar personas positivas a COVID-19 analizando espectros de saliva obtenidos por espectroscopia infrarroja transformada de Fourier (FTIR). Tras analizar 1275 espectros, con 7 estrategias comúnmente empleadas en el área de machine learning, concluimos que un modelo de regresión lineal multivariante (MLMR) resulta ser la mejor opción para identificar posibles infectados. De acuerdo con nuestros resultados, el desplazamiento observado en la región de la amida I del espectro, resulta fundamental y confiable para establecer una frontera a partir del cambio de pendiente que este provoca. Al ser más ágil y económica que la reacción en cadena de la polimerasa con transcriptasa inversa (RT-PCR), podría aplicarse confiablemente como estrategia preliminar a RT-PCR.

Caracterización biomolecular mediante microespectroscopía FTIR en la fase de remodelación de la cicatrización en un modelo murino de lesión excisional / Biomolecular characterization by FTIR microspectroscopy in the modeling phase of wound cicatrization in a murine model of excisional injury

La cicatrización de la piel es un proceso complejo y organizado que involucra tres fases: inflamatoria, proliferativa y de remodelación. Es indispensable el análisis de este proceso biomolecularmente para investigar y proponer nuevas estrategias terapéuticas que mejoren la cicatrización o promuevan la regeneración. El objetivo de este proyecto fue analizar histológica y biomolecularmente mediante microespectroscopía infrarroja por transformada de Fourier (MFTIR) y su función de mapeo bioquímico, muestras de lesiones excisionales de piel, comparando los cambios morfológicos y espectroscópicos entre piel sana y piel cicatrizada. Se estandarizó un modelo de lesión excisional de piel en ratones hembra de la cepa NIH de 8 semanas de edad (n=16), provocando una herida excisional de 1 cm2. Se analizó piel sana (día 0) y cicatrizada (día 15 post-lesión) morfométrica, histológica y biomolecularmente mediante análisis fotográfico, técnica histológica y MFTIR con su función de mapeo. El análisis morfométrico demostró una reducción del área de la herida en un 87,6 % al día 15 post-lesión. Histológicamente, en la piel cicatrizada se evidenció un adelgazamiento de la epidermis y menor celularidad en la dermis, observándose la formación de tejido de granulación y fibras de colágena desorganizadas. Espectroscópicamente, se apreciaron cambios entre los dos grupos de estudio, principalmente en las bandas de lípidos y en la región de proteínas. El cálculo de las áreas bajo la curva y el mapeo bioquímico mostraron menor concentración de queratina y colágena en la piel cicatrizada, así como desorganización de las fibras de colágena. Se demostró la capacidad de la MFTIR para caracterizar de forma precisa los cambios biomoleculares en la cicatrización, entre ellos la cantidad de queratina, colágena, y el depósito y ordenamiento de las fibras de colágena asociadas a su maduración.

The skin cicatrization is a complex and organized process that involves three phases: inflammatory, proliferative, and remodeling. It is essential to analyze this process biomolecularly, in order to investigate and propose new therapeutic strategies that improve the healing or promote regeneration. The objective of this project was to analyze histological and biomolecularly through Fourier Transform infrared microspectroscopy (FTIRM) and its biochemical mapping function, samples of an excisional skin wound, comparing the morphological and spectroscopic changes between healthy skin and scarred skin. An excisional skin wound healing model was standardized using female, NIH strain 8-week-old mice (n = 16), provoking an excisional wound of 1 cm2. Healthy skin (day 0) and scarring skin (day 15 post-injury) were morphometrical, histological, and biomolecularly analyzed by digital picture analysis, histological technique, and FTIRM with its mapping function. The morphometric analysis showed a reduction of the wound area of 87.6 % at day 15 after wound. Histologically, in the scarred skin a thinning of the epidermis was evidenced, besides reduced cellularity in the dermis, granulation tissue formation, and disorganized collagen fibers were observed. Spectroscopically, changes between the study groups were appreciated, mainly in the lipid bands and in the protein region. The calculation of the areas under the curve and the biochemical mapping showed a lower concentration of keratin and collagen in the scarred skin, as well as collagen fibers disorganization. The ability of the FTIRM to accurately characterize biomolecular changes in cicatrization process was demonstrated, such as the amount of keratin, collagen, and the deposition and ordering of the collagen fibers associated with their maturation.

La fecundación in vitro: Louise Brown, a cuatro décadas de su nacimiento / In vitro fertilization: Louise Brown, four decades after her birth

Resumen Hace 40 años, Patrick Steptoe, Robert Edwards y Jean Purdy lograron el primer nacimiento humano mediante fertilización in vitro (FIV). La FIV es una de las tecnologías transformadoras del siglo XX, diseñada para ayudar a la concepción humana e involucra cuatro aspectos principales: 1. Adquisición de un número suficiente de ovocitos mitótica y citoplasmáticamente maduros; 2. Fertilización de estos ovocitos maduros in vitro; 3. Cultivo de los embriones antes de ser implantados; 4. Transferencia embrionaria dentro del útero materno. La historia de la colaboración de Steptoe y Edwards en sus primeros años fue de decepción y fracasos, llegándose a culminar con éxito después de un total de 102 transferencias de embriones fallidas con el nacimiento de una niña llamada Louise Brown. Debido a este éxito obtenido, Robert Edwards, en el 2010, recibió el Premio Nobel de Fisiología o Medicina por el desarrollo de la FIV más transferencia de embriones (FIV / TE). Su trabajo dio como resultado el nacimiento del primer bebé «probeta¼ en julio de 1978. Ahora, más de cuatro millones de bebés han nacido empleando FIV / TE, y se ha creado una alta especialidad médica denominada Biología de la Reproducción, que se encarga de la fertilización asistida.

Abstract Forty years ago, Patrick Steptoe, Robert Edwards, and Jean Purdy achieved the first human birth through in vitro fertilization (IVF). IVF is one of the transformative technologies of the 20th century, designed to help human conception, and involves four aspects: 1. Acquisition of a sufficient number of mitotic and cytoplasmically mature oocyte. 2. In vitro fertlization of these mature oocytes; 3. Embryo culture before implantation; 4. Embryo transfer within the maternal womb. The story of the collaboration of Steptoe and Edwards was full of disappointment and failure, reaching a successful conclusion with the birth of a girl named Louise Brown, after 102 failed embryo transfers. Due to this success, Robert Edwards, in 2010, received the Nobel Prize in Physiology or Medicine for the development of IVF plus embryo transfer (IVF / ET). His work resulted in the birth of the first «test tube baby¼ in July 1978. Now, more than four million babies have born using IVF / ET, and a medical speciallity called Biology of Reproduction has been created, which is responsible of the assisted fertilization.

Genetic, Protein and FTIR Spectroscopic Comparison of Anterior and Posterior Deciduous Dental Pulp for Subsequent Obtention of SHED

Background: Stem cells from Human Exfoliated Deciduous teeth (SHED) were identified by Miura in 2003. SHED have been described as a suitable, accessible and potential source for regenerative medicine and therapeutic applications. However, the best group of deciduous teeth for the obtention of stem cells (SCs) has not been established. Therefore, this research aimed to determine the dental organs group from which SHED can be obtained with higher potentiality, considering their biomolecular features. Methodology: Deciduous teeth from 64 healthy children were collected and divided into two groups: anterior and posteriors. Dental pulp tissue was removed to determine their genetic, phenotypic, and spectroscopic profiles by RT-qPCR, immunofluorescence, and Fourier Transform Infrared (FTIR) spectroscopy respectively. Results: The results showed a higher gene (CD73 and NANOG) and protein (NANOG and SOX2) expression of mesenchymal and pluripotent markers in anterior SHED. CD146 gene expression between the two groups shows no statistical significant difference. Furthermore, the analysis of deciduous dental pulps by FTIR spectroscopy showed spectral bands related to biological samples, indicating the higher state of potentiality in anterior deciduous dental pulps. Conclusion: The deciduous dental pulp harbor a heterogenous population of SCs with different potentiality; however, the expression of multipotent and pluripotent markers was higher in the pulps from anterior deciduous teeth respect to posterior deciduous teeth. The storage and obtention of SHED from anterior teeth is more recommended respect to posterior teeth. However, it is necessary to analyze more stem cell markers and to study the differentiation capability of SHED.

Morphological, molecular and FTIR spectroscopic analysis during the differentiation of kidney cells from pluripotent stem cells

BACKGROUND: Kidney diseases are a global health problem. Currently, over 2 million people require dialysis or transplant which are associated with high morbidity and mortality; therefore, new researches focused on regenerative medicine have been developed, including the use of stem cells. RESULTS: In this research, we generate differentiated kidney cells (DKCs) from mouse pluripotent stem cells (mPSCs) analyzing their morphological, genetic, phenotypic, and spectroscopic characteristics along differentiation, highlighting that there are no reports of the use of Fourier transform infrared (FTIR) spectroscopy to characterize the directed differentiation of mPSCs to DKCs. The genetic and protein experiments proved the obtention of DKCs that passed through the chronological stages of embryonic kidney development. Regarding vibrational spectroscopy analysis by FTIR, bands related with biomolecules were shown on mPSCs and DKCs spectra, observing distinct differences between cell lineages and maturation stages. The second derivative of DKCs spectra showed changes in the protein bands compared to mPSCs. Finally, the principal components analysis obtained from FTIR spectra allowed to characterize chemical and structurally mPSCs and their differentiation process to DKCs in a rapid and non-invasive way. CONCLUSION: Our results indicated that we obtained DKCs from mPSCs, which passed through the chronological stages of embryonic kidney development. Moreover, FTIR spectroscopy resulted in a non-invasive, rapid and precise technic that together with principal component analysis allows to characterize chemical and structurally both kind of cells and also discriminate and determine different stages along the cell differentiation process.