João M Sanches

• Doctor of Philosophy
• Professor (Full) at Instituto Superior Técnico

SpO2 monitoring is a non-invasive measure of blood oxygen saturation levels, particularly important to monitor respiratory and heart circulatory diseases. Incorporating SpO2 measurement into smartphones has the potential to improve patient access and cost-effective monitoring of health status. This paper presents a new smartphone camera-based photo...

Depressive disorders are a leading cause of morbility and disability in the working population worldwide. Psychiatric assessment and treatment of depressive disorders may be improved by using objective behavioral and physiological biomarkers. In this work we present a psychiatry telemedicine platform where two important biomarkers of depression, ey...

With the beginning of the COVID-19 pandemic in early 2020, there was a pressing need for simple yet effective remote monitoring solutions. In this paper, we describe a low-cost device developed for monitoring COVID-19 patients. The device uses an ESP32 module and integrates two distinct off-the-shelf biomedical sensors: a pulse oximeter by MAXIM, a...

Depression is the leading cause of inability within the active population. The way depression is currently diagnosed is based on the clinician’s subjective examination of patient’s mental status and thus lacks biomarkers to support medical decision. Psychomotor retardation is one of the nine symptoms that are part of DSM-V criteria for major depres...

The use of ultrasound (US) as an imaging technique is essential for the diagnosis of atherosclerotic cardiovascular disease (ASCVD), which depends on US images of the carotid artery. However, US images are plagued by a specific type of noise called Speckle noise, which lowers image quality dramatically. As an attempt to improve US image quality, th...

Non-expensive methods for measuring heart rate and oxygen saturation are of great importance in the scope of the COVID-19 outbreak to follow up on the symptoms and help to control the disease.Smartphones are widely available and their cameras can be used to acquire relevant physiological data, such as Photo-plethysmography (PPG) signals. Covering a...

The cell nucleus is a tightly regulated organelle and its architectural structure is dynamically orchestrated to maintain normal cell function. Indeed, fluctuations in nuclear size and shape are known to occur during the cell cycle and alterations in nuclear morphology are also hallmarks of many diseases including cancer. Regrettably, automated rel...

In 2019, a new virus, SARS-CoV-2, responsible for the COVID-19 disease, was discovered. Asymptomatic and mildly symptomatic patients were forced to quarantine and closely monitor their symptoms and vital signs, most of the time at home. This paper describes e-CoVig, a novel mHealth application, developed as an alternative to the current monitoring...

Force transmission throughout a monolayer is the result of complex interactions between cells. Monolayer adaptation to force imbalances such as singular stiffened cells provides insight into the initiation of disease and fibrosis. Here, NRK‐52E cells transfected with ∆50LA, which significantly stiffens the nucleus. These stiffened cells were sparse...

COVID-19 has infected 77.4 million people worldwide and has caused 1.7 million fatalities as of December 21, 2020. The primary cause of death due to COVID-19 is Acute Respiratory Distress Syndrome (ARDS). According to the World Health Organization (WHO), people who are at least 60 years old or have comorbidities that have primarily been targeted ar...

Atherosclerotic plaque in carotid arteries can ultimately lead to cerebrovascular events if not monitored. The objectives of this study are (a) to design a set of artificial intelligence (AI)-based tissue characterization and classification (TCC) systems (Atheromatic 2.0, AtheroPoint, CA, USA) using ultrasound-based carotid artery plaque scans coll...

Artificial Intelligence (AI), in general, refers to the machines (or computers) that mimic “cognitive” functions that we associate with our mind, such as “learning” and “solving problem”. New biomarkers derived from medical imaging are being discovered and are then fused with non-imaging biomarkers (such as office, laboratory, physiological, geneti...

Hereditary diffuse gastric cancer (HDGC) is an autosomal dominant cancer syndrome that is characterised by a high prevalence of diffuse gastric cancer and lobular breast cancer. It is largely caused by inactivating germline mutations in the tumour suppressor gene CDH1, although pathogenic variants in CTNNA1 occur in a minority of families with HDGC...

Artificial intelligence (AI) has penetrated the field of medicine, particularly the field of radiology. Since its emergence, the highly virulent coronavirus disease 2019 (COVID-19) has infected over 10 million people, leading to over 500,000 deaths as of July 1st, 2020. Since the outbreak began, almost 28,000 articles about COVID-19 have been publi...

Segmentation of cell nuclei in fluorescence microscopy images provides valuable information about the shape and size of the nuclei, its chromatin texture and DNA content. It has many applications such as cell tracking, counting and classification. In this work, we extended our recently proposed approach for nuclei segmentation based on deep learnin...

The progression of cells through the cell cycle is a tightly regulated process and is known to be key in maintaining normal tissue architecture and function. Disruption of these orchestrated phases will result in alterations that can lead to many diseases including cancer. Regrettably, reliable automatic tools to evaluate the cell cycle stage of in...

E-cadherin (CDH1 gene) germline mutations are associated with the development of diffuse gastric cancer in the context of the so-called hereditary diffuse gastric syndrome, and with an inherited predisposition of lobular breast carcinoma. In 2019, the international gastric cancer linkage consortium revised the clinical criteria and established guid...

Transaminase activity was determined by time-lapse imaging using a colourimetric reaction and image analysis. A correlation between the benzaldehyde conversion and relative luminance was determined, allowing the identification of the...

Cell nuclei segmentation is important for several applications, such as the detection of cancerous cells and cell cycle staging. The main challenges and difficulties, associated with this task, arise due to the presence of overlapping nuclei, image intensity inhomogeneities and image noise.

This paper addresses the problem of automatic seriation of mouse brain cross-sections stained with green-florescence protein (GFP). This is fundamental for the neuroscience community to help in the processing and analyzing the huge amount of experimental data. It is also a challenging problem since, during the manual procedure of cutting the brains...

Wilson's disease (WD) is an autosomal recessive disorder which is caused by poor excretion of copper in mammalian cells. In this review, various issues such as effective characterization of ATP7B genes, scope of gene network topology in genetic analysis, pattern recognition using different computing approaches and fusion possibilities in imaging an...

The aim of this study was to uncover the pathogenic relevance and the underlying molecular mechanism of a novel CDH1 variant found in a Hereditary Diffuse Gastric Cancer family (p.L13_L15del), which affects the signal peptide of E-cadherin without changing the remaining predicted sequence. We verified that p.L13_L15del cells yield low levels of E-c...

Background Basal-like breast cancer (BLBC) is a poor prognosis subgroup of triple-negative carcinomas that still lack specific target therapies and accurate biomarkers for treatment selection. P-cadherin is frequently overexpressed in these tumors, promoting cell invasion, stem cell activity and tumorigenesis by the activation of Src-Family kinase...

Immunofluorescence is the gold standard technique to determine the level and spatial distribution of fluorescent-tagged molecules. However, quantitative analysis of fluorescence microscopy images faces crucial challenges such as morphologic variability within cells. In this work, we developed an analytical strategy to deal with cell shape and size...

Germline changes in the CDH1 tumor suppressor gene predispose to diffuse gastric cancer and lobular breast cancer. In carriers of deleterious germline CDH1 variants, prophylactic gastrectomy is recommended. In case of germline missense variants, it is mandatory to assess the functional impact on E-cadherin, the protein encoded by CDH1, and to predi...

Colorectal cancer (CRC) remains one of the leading causes of cancer mortality worldwide. Regarded as a heterogeneous disease, a number of biomarkers have been proposed to help in the stratification of CRC patients and to enable the selection of the best therapy for each patient towards personalized therapy. However, although the molecular mechanism...

The role of E-cadherin in Hereditary Diffuse Gastric Cancer (HDGC) is unequivocal. Germline alterations in its encoding gene (CDH1) are causative of HDGC and occur in about 40% of patients. Importantly, while in most cases CDH1 alterations result in the complete loss of E-cadherin associated with a well-established clinical impact, in about 20% of...

The original version of this article unfortunately contained a mistake. The family name of Rui Tato Marinho was incorrectly spelled as Marinhoe. © 2017, Springer Science+Business Media, LLC, part of Springer Nature.

Background and Objective Fatty Liver Disease (FLD) - a disease caused by deposition of fat in liver cells, is predecessor to terminal diseases such as liver cancer. The machine learning (ML) techniques applied for FLD detection and risk stratification using ultrasound (US) have limitations in computing tissue characterization features, thereby limi...

The optimization formulations of sparse signal recovery problems use a regularizer term which encourages the solution to be sparse or piece-wise smooth. Of special interest are the ℓp norms with 0 ≤ p ≤ 1 which penalize large values and encourage the solution of the optimization problem to be sparse. In this work, we propose a new regularizer in wh...

Fatty Liver Disease (FLD) is caused by the deposition of fat in liver cells and leads to deadly diseases such as liver cancer. Several FLD detection and characterization systems using machine learning (ML) based on Support Vector Machines (SVM) have been applied. These ML systems utilize large number of ultrasonic grayscale features, pooling strate...

In the past decades, there has been an amazing progress in the understanding of the molecular mechanisms of the cell cycle. This has been possible largely due to a better conceptualization of the cycle itself, but also as a consequence of technological advances. Herein, we propose a new fluorescence image-based framework targeted at the identificat...

Physical forces mediated by cell-cell adhesion molecules, as cadherins, play a crucial role in preserving normal tissue architecture. Accordingly, altered cadherins' expression has been documented as a common event during cancer progression. However, in most studies, no data exist linking pro-tumorigenic signaling and variations in the mechanical b...

Scientific Reports 6: Article number: 25101; 10.1038/srep25101 published online: May 06 2016; updated: July 27 2016. In the original version of this Article, Affiliation 1 was incorrectly given as “Institute for Systems and Robotics, Instituto Superior Tecnico, Lisboa, Portugal”. The correct Affiliation is listed below: “Institute for Systems and...

In cancer, defective E-cadherin leads to cell detachment, migration and metastization. Further, alterations mediated by E-cadherin dysfunction affect cell topology and tissue organization. Herein, we propose a novel quantitative approach, based on microscopy images, to analyse abnormal cellular distribution patterns. We generated undirected graphs...

Intentions of specific motor movements are known to generate event-related (de)synchronization (ERD/ERS) patterns which may be interpreted as changes in the degree of synchronization of underlying neuronal networks. When activated, the neural populations in a certain region of the brain de-synchronize, leading to a decrease in the EEG power signal....

Objectives: Psychomotor Vigilance Task (PVT), melatonin and cortisol salivary concentrations are often used as fatigue markers. Salivary protocols to analyse synchronously different markers are very important in human research, especially due to their applications in daily routines. PVT, melatonin and cortisol present circadian variations, and pr...

Mean X-ray attenuation of salivary calculi computed from microtomography data - Volume 21 Issue S6 - P Nolasco, P. V. Coelho, A.P. Alves de Matos, A. Maurício, M.F.C. Pereira, J.M.R. Sanches, P.A. Carvalho

E-cadherin is a central molecule in the process of gastric carcinogenesis and its posttranslational modifications by N-glycosylation have been described to induce a deleterious effect on cell adhesion associated with tumor cell invasion. However, the role that site-specific glycosylation of E-cadherin has in its defective function in gastric cancer...

Ubiquitous monitoring has become a useful tool for the prevention and early diagnosis of some disorders. This kind of monitoring is nowadays very common thanks to the irruption of smartphones, which make easier the collection and delivery of the patient’s data. However, some problems arise due to the occasional low quality of the acquired data. Thi...

In some imaging modalities based on coherent radiation, the noise contaminating an image may contain useful information, thereby necessitating the separation of the noise field rather than just denoising. When the algebraic operation that relates the image and noise is known, the noise component can be estimated in a straightforward manner after de...

In this paper, we address the problem of image reconstruction with missing pixels or corrupted with impulse noise, when the locations of the corrupted pixels are not known. A logarithmic transformation is applied to convert the multiplication between the image and binary mask into an additive problem. The image and mask terms are then estimated ite...

Most sleep deprivation (S.D.) studies are conducted either with animal models or in young adults and occur in highly controlled situations (sleep laboratory). • In their regular living and working conditions these studies are however lacking. • Causes of disturbed or curtailed sleep vary, but one obvious source are the effects of daily working life...

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In this paper, we present a method for reconstructing images or volumes from a partial set of observations, under the Rayleigh distributed multiplicative noise model, which is the appropriate algebraic model in ultrasound (US) imaging. The proposed method performs a variable splitting to introduce an auxiliary variable to serve as the argument of t...

Missense mutations result in full-length proteins containing an amino acid substitution that can be neutral or deleterious, interfering with the normal conformation, localization, and function of a protein. A striking example is the presence of CDH1 (E-cadherin gene) germline missense variants in hereditary diffuse gastric cancer (HDGC), which repr...

This paper proposes a risk score computed from ultrasound data that correlates to plaque activity. It has the twofold purpose of detecting symptomatic plaques and estimating the likelihood of the asymptomatic lesion to become symptomatic. The proposed ultrasonographic activity index (UAI) relies on the plaque active profile which is a combination o...

Detection and characterization of vulnerable plaques is of paramount importance for early disease diagnosis and treatment of carotid and coronary vascular accidents, which are mostly caused by this type of plaques. In this scope, the echo-morphology and composition are described in the literature, in statistical frameworks, by using several distrib...

Stroke is one of the leading causes of death in the world, resulting mostly from the sudden ruptures of atherosclerosis carotid plaques. Understanding why and how plaque develops and ruptures requires a multi-disciplinary approach such as radiology, biomedical engineering, medical physics, software engineering, hardware engineering, pathological an...

The automatic computation of the hypnogram and sleep Parameters, from the data acquired with portable sensors, is a challenging problem with important clinical applications. In this paper, the hypnogram, the sleep efficiency (SE), rapid eye movement (REM), and nonREM (NREM) sleep percentages are automatically estimated from physiological (ECG and r...

Carotid and coronary vascular incidents are mostly caused by vulnerable plaques. Detection and characterization of vulnerable plaques are important for early disease diagnosis and treatment. For this purpose, the echomorphology and composition have been studied. Several distributions have been used to describe ultrasonic data depending on tissues,...

This chapter addresses the problem of liver cirrhosis classification via ultrasound imaging. For this classification problem, a liver semiautomatic contour segmentation algorithm to characterize the morphology and a textural feature extraction scheme for the characterization of liver parenchyma are proposed. Phase congruency is used to enhance live...

Introduction One of the prominent features in fibromyalgia patients (FMP) is the discrepancy between subjective and objective data. Pain index are more intense than in Rheumatoid Arthritis patients but supportive objective data are lacking. Sleep is among the most prevalent complaints and the intrusion of alpha activity, although common, is not spe...

Introduction The advent of small and portable devices, with high storage and processing capabilities have allowed physiological data to be acquired outside clinical environments in a reliable way, often across several days. These sources of data include ECG, Respiratory Inductance Plethysmography (RIP), oxygen saturation, Actigraphy (ACT), among ot...

Liver steatosis is a common disease usually associated with social and genetic factors. Early detection and quantification is important since it can evolve to cirrhosis. In this paper, a new computer-aided diagnosis (CAD) system for steatosis classification, in a local and global basis, is presented. Bayes factor is computed from objective ultrasou...

Active carotid plaques are associated with atheroembolism and neurological events; its identification is crucial for stroke prevention. High-definition ultrasound (HDU) can be used to recognize plaque structure in carotid bifurcation stenosis associated with plaque vulnerability and occurrence of brain ischemic events. A new computer-assisted HDU m...

Wrist actigraphy (ACT) is a low cost and well established technique for long term monitoring of human activity. It has a special relevance in sleep studies, where its non-invasive nature makes it a valuable tool for behavioural characterization and for the detection and diagnosis of some sleep disorders. The traditional sleep/wakefulness state esti...

Laser scanning fluorescence confocal microscope (LSFCM) imaging is an extensively used modality in biological research. However, these images present low signal to noise ratio and a time intensity decay effect due to the so called photoblinking/photobleaching (PBPB) phenomenon that corresponds to an intensity fading of a fluorescent probe along the...

This chapter proposes an ultrasound-based diagnostic measure to quantify plaque activity which is the likelihood of the asymptomatic lesion to produce neurological symptoms. This method, based on a classification study, first identifies the active plaque profile containing the most relevant ultrasound parameters associated with symptoms. This infor...

Structural and mechanical properties of the tissues are dependent on the physical linkage between cells. E-Cadherin is a key component on this adhesion mechanism and mutations on its coding gene may produce dysfunctional molecules that compromise the cell-cell linkage and increase the risk of cancer. The stationary distribution of E-Cadherin is cha...

This paper presents an algorithm for reconstructing a three dimensional image from a set of noisy two dimensional images, corrupted with Rayleigh distributed multiplicative noise, which is the observational model for Ultrasound imaging. The proposed method performs a variable splitting to introduce an auxiliary variable to serve as the argument of...

In the refractive assessment by optical evaluation based on ray-tracing, the definition of the best focus plane remains a challenge. We simulated 100 pseudophakic eye models using a Montecarlo analysis with ray-tracing evaluation. The image quality resulting from optimization with the Visual Strehl ratio computed in frequency domain weighted by the...

Arterial Spin Labeling (ASL) is a non-invasive technique for generating perfusion images of the brain. Following an alternating labeling/control acquisition sequence, the small magnetization difference between labeled and non-labeled images is usually detected by performing image subtraction. In order to increase the Signal to Noise Ratio (SNR) a l...

Carotid plaques are one of the commonest causes of neurological symptoms due to embolization of plaque components or flow reduction. The classification of plaques vulnerability is then a relevant clinical issue, and a technical challenge. Recently, several atherosclerotic plaque characterization methods were proposed based on plaque morphology asse...

Model for End-stage Liver Disease (MELD) is a common score used in clinical practice to estimate the prognostic outcome of cirrhotic patients. This score is obtained from laboratory results. Here a novel method is proposed to estimate the MELD score based on textural information extracted from normalized ultrasound (US) images of liver parenchyma....

In the scope of EEG applications such as Brain Computer Interfaces (BCI) or the evaluation of epileptic activity, the detection of event-related potentials (ERP) and associated event-related desynchronization / synchronization (ERD/ERS) are common goals. The most commonly used method for assessing ERD/ERS consists on the evaluation of EEG power cha...

In the case of carotid atherosclerosis, to avoid unnecessary surgeries in asymptomatic patients, it is necessary to develop a technique to effectively differentiate symptomatic and asymptomatic plaques. In this paper, we have presented a data mining framework that characterizes the textural differences in these two classes using several grayscale f...

Chronic Liver Disease (CLD) is most of the time an asymptomatic, progressive and ultimately potentially fatal disease. In this work, an automatic hierarchical procedure to stage CLD using ultrasound images, laboratory tests and clinical records is described. The first stage of the proposed method, called Clinical Based Classifier (CBC), discriminat...

Characterization of carotid atherosclerosis and classification into either symptomatic or asymptomatic is crucial in terms of diagnosis and treatment planning for a range of cardiovascular diseases. This paper presents a computer-aided diagnosis (CAD) system (Atheromatic) that analyzes ultrasound images and classifies them into symptomatic and asym...

The chapter proposes a framework for extending the analysis of the atherosclerotic disease to a three-dimensional perspective. Different data acquisition systems, either based on a robotic arm setup or free-hand are proposed, in order to collect image sequences that completely describe the plaque anatomy. A 3D reconstruction method is proposed, com...

Carotid bifurcation disease is a major cause of stroke in the western population. Atherosclerotic plaques located at the carotid bifurcation are a source of atheroembolization into the brain and may also cause flow restriction. Severity of stenosis is related with the risk of stroke as shown in multicenter studies. Nevertheless, in asymptomatic dis...

Many learning problems require handling high dimensional datasets with a relatively small number of instances. Learning algorithms are thus confronted with the curse of dimensionality, and need to address it in order to be effective. Examples of these ...

Recently, several atherosclerotic plaque characterization methods were proposed based on plaque morphology assessed through 2D ultrasound. It is of extreme importance to establish an objective quantification measure which allows the physicians to determine the risk of plaque rupture, and thus, of brain stroke. Having these, sometimes complex, measu...

Wrist actigraphy is a well established procedure to monitor human activity. Among other areas, it has a special relevance in sleep studies where its lightweight and non-intrusive nature make it a valuable tool to access the circadian cycle. While there are several methods to extract information from the data, the differentiation between sleep and w...

A Brain-Computer Interface (BCI) attempts to create a direct channel of communication between the brain and a computer. This is especially important for patients that are "locked in", as they have limited motor function and thus require an alternative means of communication. In this scope, a BCI can be controlled through the imagination of motor ta...

Automatic Karyotyping is the process of classifying chromosomes from an unordered karyogram into their respective classes to create an ordered karyogram. Automatic karyotyping algorithms typically perform geometrical correction of deformed chromosomes for feature extraction; these features are used by classifier algorithms for classifying the chrom...

Liver steatosis is a common disease usually associated with social and genetic factors. Early detection and quantification is important since it can evolve to cirrhosis. Steatosis is usually a diffuse liver disease, since it is globally affected. However, steatosis can also be focal affecting only some foci difficult to discriminate. In both cases,...