The aim of oral cancer surgery is tumor removal within clear margins of healthy tissue: the latter definition in the literature, however, may vary between 1 and 2 cm, and should be intended in the three dimensions, which further complicates its precise measurement. Moreover, the biological behavior of tongue and floor of mouth cancer can be unpredictable and often eludes the previously mentioned safe surgical margins concept due to the complexity of tongue anatomy, the intricated arrangements of its intrinsic and extrinsic muscle fibers, and the presence of rich neurovascular and lymphatic networks within it. These structures may act as specific pathways of loco-regional tumor spread, allowing the neoplasm to escape beyond its visible macroscopic boundaries. Based on this concept, in the past two decades, compartmental surgery (CS) for treatment of oral tongue and floor of mouth cancer was proposed as an alternative to more traditional transoral resections.The authors performed three anatomical dissections on fresh-frozen cadaver heads that were injected with red and blue-stained silicon. All procedures were documented by photographs taken with a professional reflex digital camera.One of these step-by-step cadaver dissections is herein reported, detailing the pivotal points of CS with the aim to share this procedure at benefit of the youngest surgeons.We herein present the CS step-by-step technique to highlight its potential in improving loco-regional control by checking all possible routes of tumor spread. Correct identification of the anatomical space between tumor and nodes (T-N tract), spatial relationships of extrinsic tongue muscles, as well as neurovascular bundles of the floor of mouth, are depicted to improve knowledge of this complex anatomical area. This has been demonstrated to achieve optimal loco-regional control, while not substantially impacting functional outcomes and residual quality of life  has emerged in the last decade as a promising approach for treatment of locally advanced cancers of the tongue and floor of mouth. The term “compartmental” has been borrowed from the field of sarcoma surgery which typically aims to remove an entire anatomical compartment defined as an entire group of muscle fibers, vascular, lymphatic and neural bundles along with the overlaying fascial system that usually drive tumor growth and direction, following the spatial orientation of these structures , 2. Firs of life –7.The ideal indications for CS are represented by tongue and/or floor of mouth cancers with a clinical/radiological depth of infiltration (DOI) ≥10 mm (as ascertained by preoperative MR or CT scans with contrast administration). The importance of a DOI threshold ≥10 mm for tongue cancer has been demonstrated to be crucial in various clinical and anatomical studies, clearly showing that the boundary between the vast majority of intrinsic and extrinsic muscle fibers in such a complex anatomy mainly occurs at this depth –11. HoweWe herein present the CS technique in a step-by-step fashion, based on a fresh cadaver dissection focusing on the most valuable anatomical details, in order to make it possible for the reader to reproduce the procedure in an oncologically safe way in routine clinical practice.®, Portland, Oregon, USA) were dissected in the Laboratory of Anatomy at the University of Brescia, Italy. The arterial and venous systems had been previously injected with red and blue-stained silicon, respectively. A complete set of head and neck surgical instrumentation was available for the dissection. All the anatomical procedures were recorded by a VITOM 3D  or a 4K endoscope  for academic purposes. The photographs of all anatomical dissections for each step were taken using a reflex digital camera with a 12.3 megapixel resolution  coupled with a 60 mm F/2 Macro 1:1 fixed focal length lens, mounted on a tripod.Three fresh-frozen cadaver heads  . As a consequence, the internal jugular vein (IJV) and common carotid artery (CCA) with its bifurcation are fully visible when retracting the sternocleidomastoid muscle (SCM). The external carotid artery (ECA) with its collateral branches is also in full view. Thyroid and occipital arteries (the latter resected) and their anatomical relationships with the XII cranial nerve can be easily appreciated.The digastric muscle with its anterior (ABDM) and posterior bellies (PBDM) is skeletonized to correctly delimitate the inferior borders of the submandibular space. The submandibular gland and adjacent fat tissue containing lymph nodes of level IB is then dissected from the surrounding tissues and detached from the mylohyoid muscle (MhM), which represents the deep plane of dissection. Facial artery (FA) and its submental branch (SmA) are found herein and, whenever possible, preserved  are dissected and preserved as long as possible since they represent the first option for subsequent micro-anastomoses during the reconstructive phase.The patient is positioned supine with the head extended and turned in order to expose the affected neck side.In short necks, it is advisable to put a roll under the patient’s shoulders to further improve neck extension.The FA is ligated to clearly expose the submandibular space. The MhM is completely skeletonized, identifying its bony attachment to the mandible and hyoid bone. The intermediate tendon of the digastric muscle (ITDM) is pulled down along with the stylohyoid muscle (StM) in order to highlight the lingual artery (LA) and the XII cranial nerve. This space, also known as Pirogov’s triangle, is bounded by the ITDM, posterior margin of the MhM, and XII cranial nerve cranially. The LA is clearly visible close to its branching point from the ECA while, after 1-2 cm, it lays deep to the hyoglossus muscle (HgM) . The former is identified from posterior to anterior crossing the ECA, running deeply to the PBDM and StM, and superficially to the HgM (hidden by the silicone background) and LA. Two centimeters cranially and anteriorly, running deeply to the MhM, the LN can be found in close relationship with the sublingual gland and floor of mouth mucosa. The XII cranial nerve must be followed and sectioned, preserving, if feasible, the emergence of its descending loop with the cervical plexus to maintain the strap muscles innervation Figure 3Surgical tips and tricksFrozen sections should be sent from the cranial stump of the hypoglossal nerve, especially in the presence of advanced cancers massively infiltrating the MhM and HgM.Identification of the HgM is made easier by gripping the hyoid bone with Ellis forceps and pulling it laterally.The LA must be ligated and frozen sections sent for possible vascular invasion evaluation, especially when floor of the mouth gross involvement is detected. This maneuver will also greatly reduce bleeding during subsequent tongue resection. The LA can be also used as an alternative to the FA as a donor vessel for microvascular anastomoses.The anatomical preservation of the descending loop of the XII cranial nerve may improve swallowing in the postoperative period.Once the above mentioned neurovascular structures have been identified, the dissection proceeds delimitating the T-N tract from caudal to cranial following the bony attachments of the different muscular structures. In this specific case, the digastric muscle has been removed to better expose the extrinsic lingual muscular compartment . The LA, clearly visible at the level of its branching from the ECA, is followed through the HgM (grabbed with forceps), and detached from its hyoid insertions (black dotted line). Cranially, the MhM has been detached from the mylohyoid line (white dotted line) on the internal aspect of the mandibular body, while the LN is exposed and sectioned as cranial as possible. Anteriorly, the ABDM is retracted medially to show the fatty median raphe between the left and right genioglossus muscles (GgM). Anteriorly and superficially the geniohyoid muscle (GhM) and deeply both the GgMs are well visible. Lateral to the right GgM the fat-containing paramedian septum is recognizable (black arrow) Figure 4Surgical tips and tricksIf not oncologically required, it is not advisable to completely skeletonize the hyoid bone, especially in previously irradiated patients, to reduce the risk of postoperative osteonecrosis.Conversely, when detaching the MhM from the inner mandibular surface, it is advisable to use monopolar cautery, taking care to cut the fibers directly over the bone in a subperiosteal plane . This is of paramount importance, especially when managing tumors involving the antero-lateral floor of the mouth, with close relationship to the mandible, even without radiological signs of erosion, in order to assess a possible limited cortical bone or periosteal neoplastic invasion.Once the lateral compartment has been prepared, the head is turned to a neutral position while extended in order to fully expose the region from the hyoid bone up to the mandible. The midline is found by sectioning the MhM in between the two ABDMs. The section line , and branches of the sublingual artery (SLA)  mucosa cranially, the GhM anteriorly, and the HB caudally (black dotted line) Figure 6Surgical tips and tricksWhen approaching the MhM, it can be difficult to properly identify its midline since the muscle fibers of both sides at this level are usually merged. An easy way for its correct identification is therefore to cut with electrocautery a line running from the genial tubercles to the midline of the HB identified by palpating the thyroid notch.Once the MhM is detached from the deeper GhM, particular care should be addressed to obtain accurate hemostasis due to the large number of small perforators between the two muscles. Keeping the surgical field as clean as possible in this phase may be of great help in correctly identifying the median raphe and contralateral muscular compartment.Once the GhM has been resected, the midline fibrous raphe between the two hemilingual compartments is clearly recognizable. It is imperative to not resect muscular or neurovascular structures of the healthy side in order to minimize any undue functional impairment. Separation of the two compartments at this level is usually easily obtained by blunt dissection, using a cotton swab or dissector. This maneuver is also useful to palpate the lingual body from below in order to assess the tumor characteristics and possible critical issues such as endophytic extension, distance from the midline, or presence of satellitosis. The insertion of the removed right GhM is visible at the level of the inferior genial tubercle (arrow), while the deeper extrinsic muscular layer (represented by the GgM) is now clearly visible , caudal (HB), contralateral , and posterior/cranial insertions (mastoid and styloid processes). The most important advantage of CS is that it allows the most adequate control of all possible routes for centrifugal tumor spread that, starting from posterior to anterior, in an anti-clockwise direction, are shown herein: 1) SgM (towards the skull base), 2) XII cranial nerve (towards the vascular axis and skull base), 3) LA (towards the vascular axis), 4) HgM (towards the HB), and 5) GgM (towards the mandible) Figure 9via the transoral route up to the circumvallate papillae in most patients without trismus  has been prepared from the neck, it is possible to access the tumor through the oral cavity. The operating surgeon moves to the patient’s head and dissection starts from the anterior FoM, between the two openings of the Wharton’s ducts. A communication with the underlying neck space is created at this level and identification of the gauze previously positioned from the neck helps the surgeon to complete the dissection in the correct plane. Next, resection proceeds in a caudo-cranial direction, towards the ventral and dorsal surfaces of the tongue, maintaining the tumor under direct vision/palpation, and strictly following the midline lingual raphe. Dissection can be safely carried The T-N tract, completely released from all its muscular insertions and neural/vascular supplies, is visible as composed by the sublingual and submandibular glands (previously removed), extrinsic tongue muscles  and MhM, LA and vein, XII cranial nerve, LN, and the lymphatic vessels and nodes embedded in the median and paramedian septa  should be performed to remove the tube from the oral cavity and thus secure the postoperative airways. In some cases, this step can be postponed at the end of surgery if nasotracheal intubation has been performed. Others prefer to perform tracheostomy at the beginning of surgical procedure, to avoid any possible neoplastic seeding at the level of the tracheal wound by “contaminated” instrumentation. In any case, before starting the transoral step, the anesthesiologist should provide an optimal muscle relaxation in order to maximize oral opening.A self-retaining mouth and lips retractor and/or bite blocks can be used to optimize the view of the surgical field.Electrocautery or ultrasonic scalpels are usually applied to reduce bleeding during this phase, especially at the level of the contralateral  hemilingual compartment.The tip of tongue can be spared when not directly involved by the tumor since it is composed only of intrinsic muscles and not anatomically reached by the GgM fibers. This definitively improves postoperative speech without affecting oncologic outcomes.When sampling tissue for frozen sections, especially along the midline of the oral tongue, it is advisable to use a cool blade knife to reduce the shrinkage and cautery/crush artifacts of the specimen to be analyzed.When dissection between the two openings of the Wharton’s duct in the anterior aspect of the FoM is performed, particular attention should be paid to not accidentally injure the healthy side. The same holds true when suturing, at the end of surgery, the free flap at this level.Whenever the midline is reached by the tumor without invasion of the opposite side, a cuff of extrinsic/intrinsic muscles of the healthy hemilingual compartment should be taken as a safe extra-margin.When lateral FoM mucosa is incised medial to the mandibular body, at least 5 mm of healthy tissue should be spared at this level, if oncologically feasible, in order to guarantee enough recipient mucosa for the in-set of the free flap. If this is not possible, suturing the flap cutaneous edge to the mucosa of the gum passing the stitches in between teeth can be used as an effective trick to reduce the risk of salivary fistula.via transoral or transmandibular routes.For tumors massively involving the BoT and/or associated with severe trismus, a median/paramedian mandibulotomy to widen the surgical field and guarantee an optimal visualization and dissection of the tumor may be of great help. All the steps herein described for CS can be equally performed At the end of procedure, the surgical defect results in a wide communication between oral cavity/oropharynx and neck, delimited by the symphysis and body of the mandible anterolaterally, constrictor muscles and tonsillar region posteriorly, HB and glosso-epiglottic vallecula inferiorly, and healthy contralateral tongue compartment medially , ipsilateral FoM with related T-N tract, and the distal fringes of all the extrinsic muscles  anatomically-based approach to the lesion within the tongue and floor of mouth compartment, aiming to control all potential pathways of tumor progression; 2) clear identification of the anatomical space between primary and cervical nodes , potentially acting as a high-risk metastatic basin; 3) good reproducibility and standardization of the surgical technique. A rational resectional approach associated with modern microsurgical reconstructive techniques maximizes oncological outcomes, while not affecting the mobility and function of the contralateral healthy hemitongue.The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.Study design: all authors. Anatomical dissections: AG, CP, MF, VV, LC. Drafting of the manuscript: all authors. Revision of the manuscript: AG, CP, AP, LC. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


The aim of this research is to analyze the relationship between executive functions and adaptive behavior in girls with Fragile X syndrome (FXS) in the school setting. This study is part of a larger investigation conducted at the Hospital Parc Tauli in Sabadell. The sample consists of a total of 40 girls (26 with FXS and 14 control) aged 7–16 years, who were administered different neuropsychological tests  and questionnaires answered by teachers . The results show that there is a greater interaction between some areas of executive function  and certain areas of adaptive behavior  in the FXS group than in the control group. These results suggest that an alteration in the executive functions was affecting the daily functioning of the girls with FXS to a greater extent. Fragile X syndrome (FXS) is the most common cause of sex-linked inherited intellectual disability. It is a genetic condition that occurs as a consequence of amplification of the CGG triplet of the FMR1  gene located on Xq27.3 [The clinical phenotype usually presents more severely in males than in females, since in females the unaffected X chromosome can synthesize some amount of FMRP . This faIn the case of females affected by FXS, we found a great variability in their neurocognitive phenotype. Their intellectual ability can range from intellectual disability (mild–moderate) to within the average . A totalIn much of the research carried out to date, executive function (EF) is described as a domain of cognitive weakness in girls with FXS. EF is a construct that encompasses a set of skills needed to carry out a goal directed behavior. Attention, inhibitory control, working memory, cognitive flexibility, processing speed, and planning are included . AttentiIn a systematic review it was found that girls with FXS presented worse performance in working memory tasks, inhibitory control, and processing speed that the control group (CG) . AnotherIn another study of 50 women aged between 18 and 58 years  it was found that women with FXS obtained significantly lower IQ scores. The results obtained also suggest a deficit in verbal working memory in the group of women with FXS . Along sAdaptive behavior is defined as the set of conceptual, social, and practical skills that people learn to be able to function in daily life. In other words, it is the degree or effectiveness with which people meet the requirements of independence and social responsibility expected for their age and cultural group . In feman = 18) and Turner syndrome (n = 16). No significant differences were found between the two groups, and it was concluded that the poorer performance in the tasks used to assess EF was attributable to their IQ and not to the fact of presenting the FXS condition. Despite there being no significant differences between the groups, it was concluded that EF  are related to basic daily living skills [Only two studies were found that focused on the influence of EF on independent living skills. The first studied the role of EF in independent living skills in adolescents and young adults with FXS . The Parc Tauli Hospital, the Spanish FXS Federation, different associations of patients with FXS , and patients with genetic diseases (D’Genes Murcia) collaborated in the dissemination of the project to facilitate the recruitment of participants. Likewise, a call was made via professional social networks such as Linked-In and emails sent to the psycho-pedagogical advisory teams in the area and to the special education colleges.Informed consent was obtained from the legal guardians of all the participants. The tests to be performed on the young girls and adolescents were also explained. If they had refused to perform the tests, the evaluation would not have been carried out. All of them verbally agreed to perform the tests.-n = 26. Participants recruited through the Parc Tauli Hospital and the different patient associations.FXS group: -n = 14. Participants were recruited through outpatients’ appointments at the Neuropediatric Unit of Sabadell’s Parc Tauli Hospital and standard and special education schools in the area.Control group (CG): A total of 40 girls aged between 7 and 16 years took part in the study. They were divided into the following two groups:The inclusion and exclusion criteria were as follows:-FXS group: female, aged between 7 and 16 years, FXS confirmed by genetic study (>200 repetitions).-Control Group: female, aged between 7 and 16 years.-FXS criteria: presence of comorbid autism spectrum disorder (ASD) or ADHD, absence of expressive language, acquired neurological disorders .-Control Group: meeting the diagnostic criteria for ASD or ADHD, absence of expressive language, acquired neurological disorders  and other cognitive-behavioral disorders. Participants without ID did not undergo a genetic study for ethical reasons, but the subjects were questioned explicitly about their family history of FXS and the presence of clinical symptoms compatible with an FXS diagnosis.In both groups, participants who met all the DSM-5 criteria for the diagnosis of ASD and ADHD were excluded from the sample. Participants who only showed some symptoms were not excluded. The assessment was performed by an expert in pediatric neurology, psychology, or psychiatry.The assessment sessions for the participants from the Barcelona Metropolitan Area took place in Sabadell’s Parc Tauli Hospital. The lead investigator travelled to the autonomous regions where the rest of the participants lived to carry out the assessments, thus ensuring as little inconvenience as possible for the participants and their families. The participating autonomous communities were Catalonia, Madrid, the Basque Country, Galicia, Valencia, and Murcia.First, a document explaining the project was produced and sent to the patient associations for dissemination among the families. When a family showed interest in taking part in the study, the lead investigator would travel to the pertinent autonomous region on previously agreed days to carry out the assessments in the facilities provided by the associations. The assessment was divided into three separate one-hour sessions to ensure that participants did not become overtired. Last, teachers were asked to complete the corresponding questionnaires. Due to the general and reading comprehension difficulties shown by most of the subjects, the administration of self-reported questionnaires was not possible.The Wechsler Intelligence Scale for Children-V was used to assess General Cognitive Ability .The following aspects of executive function were used as independent variables: Visual Working Memory (WISC-V. Picture Span subtest), Auditory Working Memory (WISC-V. Digits and Letters and Numbers subtest) ; AuditorThe following questionnaires and scales were used to assess the behavioral variables: ADHD Rating Scale (teachers’ version) to assess the ADHD Symptomatology  and the ® PCR/CE FMR1 kit is an in vitro diagnostic tool designed for professional use in clinical laboratories to amplify and detect the cytosine-guanine-guanine triplet (CGG) repeat sequences in the 5′ untranslated regions of the Fragile X mental retardation gene 1 (FMR1). The kit is intended as an aid in diagnosing Fragile X syndrome and associated disorders such as tremor/ataxia syndrome (FX-TAS), and primary ovarian insufficiency (FX-POI) through determination of the number of CGG repeats up to 200 CGGs and detection of alleles with more than 200 CGGs. The test consists of a polymerase chain reaction (PCR) of genomic DNA purified from whole blood or buccal cells, followed by fragment measurement on a general laboratory-validated genetic analyzer or capillary electrophoresis platform, and conversion of product size to the number of CGG repeats. The kit includes reagents to perform 2 types of PCRs: gene-specific PCR (GS-PCR) and PCR with CGG repeat primers. Gene-specific PCR uses two primers that span the CGG repeat region. The PCR products from the gene-specific primers represent full-length alleles. PCR with CGG repeat primers differs from the more conventional gene-specific PCR by the addition of a third primer, which is complementary to the triplet repeat region of the FMR1 gene. The resulting electropherogram includes the full-length PCR products generated from the gene-specific primers spanning the CGG repeat region and the CGG repeat peaks obtained by RP PCR. The full-length gene-specific peaks are similar in the two methods. The PCR products with CGG repeat primers correspond to the individual PCR amplicons of each combination of the repeat primer with the reverse primer. The peaks corresponding to the CGG repeats are separated by 3 bp, as expected. The peak profile provides confirmatory information about a sample, including zygosity and the presence of interspersed AGG sequences.At Hospital Parc Tauli, genetic studies are performed using the Asuragen commercial kit, which includes two PCRs. The AmplideXThe statistical analysis was carried out using the SPSS Statistics for Windows Version 25.0 software.2 > 0.60.Student′s t-test was used for the demographic data and the control variables . For the binary variables, an interaction model was made by creating contingency tables between the tests performed with the patients and the questionnaires filled out by the teachers, comparing the group of girls with FXS and the control group with a 95% confidence interval, and the variables were also selected by adjusted rRegarding IQ, 50% of the participants in the FXS group in our sample scored in the range of mild/moderate ID, while the remaining 50% scored in the medium/medium-low range. No significant differences were found in the control variables age, IQ, ADHD symptoms, and socioeconomic status. .Once the data were analyzed, statistically significant differences were found between the two groups, with the FXS group presenting a stronger relationship between certain EF and some adaptive behavior skills.A relationship was found between the following variables: visual abstraction ability and conceptual, practical, social, and total adaptive behavior domains. Correct auditory attention and social and practical domains. Auditory attention commission errors and conceptual, social, practical, and total adaptive behavior domains. Auditory attention omission errors and social and practical domains. Auditory attention inhibition errors and practical domain. Correct cognitive flexibility and social and practical domains. Cognitive flexibility errors of commission and conceptual, social, practical, and total adaptive behavior domains. Cognitive flexibility omission errors and total adaptive behavior domain. Cognitive flexibility inhibition errors and social and practical domains. Global index of executive function and conceptual), social, practical, and total adaptive behavior domains .The aim of the present research was to study the relationship between EF and performance in adaptive behavior at school. Having analyzed the results, we can conclude that cognitive flexibility and auditory attention are two areas of EF that have a greater influence on adaptive behavior in girls with FXS than on the CG.Both variables were obtained from the auditory attention and cognitive flexibility subtest of the NEPSY-II battery. Focusing on the errors of commission of both tests, the authors point out that these may be due to impulsivity, inattention, or slow response . ConsideFocusing on the omission errors, in this case the relationship is with the social, practical, and total adaptive behavior domains in the case of cognitive flexibility, and with the social and practical domains in the case of auditory attention. Poor performance in this test may be due to low vigilance . Being aNext, we discuss the inhibition errors, which affect the social and practical domains in the case of cognitive flexibility and only the practical domain in the case of auditory attention. These errors may be due to impulsivity or difficulty in switching from a previously learned behavior to a new response . A betteRegarding the correct answers, the relationship was found with the social and practical domains of adaptive behavior in the cases of both cognitive behavior and auditory attention. Cognitive flexibility is very important in any social relationship to be able to adapt to turns and changes of conversation, game rules, etc. Auditory attention is also essential since the auditory channel is fundamental for oral communication. The practical domain is the one that would encompass more basic activities of daily life such as self-care and handling money to go shopping. To carry out these types of activities effectively, it is essential to be able to communicate with the people around us  and to know how to change from one activity to another during the day.Furthermore, a relationship was found between visual abstraction capacity and all domains of adaptive behavior . These results are in line with those found by Joga et al. (2021), where it was found that a better verbal abstraction ability has a positive impact on the domain of conceptual adaptation . To thisLast, a relationship was found between global executive functioning  and all domains of adaptive behavior , which indicates that having executive dysfunction had a greater impact on all areas of adaptive behavior in the girls of the FXS group.One of the limitations of this study is the relatively small size of the sample. However, despite only 26 girls with FXS participating in the study, it is still the largest sample of girls of child-juvenile age collected to date in Spain, and one of the largest at an international level.Another limitation was the great difficulty we had in finding many girls for the CG. Nonetheless, there were no significant differences between the groups in terms of the control variables, age, IQ, ADHD symptoms, and socioeconomical status.Furthermore, while the girls with ID in the control group had undergone a genetic analysis ruling out FXS, at no time did the girls without ID undergo a genetic study for ethical reasons. However, the participants were evaluated clinically to assess whether they presented symptoms compatible with FXS , and they were asked specifically about any previous family history of FXS.The results show that there is a greater interaction between some areas of executive function  and certain areas of adaptive behavior  in the FXS group than in the control group. These results suggest that an alteration in the executive functions was affecting the daily functioning of the girls with FXS to a greater extent.


Here we demonstrate a method for solving genome assembly tasks with the use of quantum and quantum-inspired optimization techniques. Within this method, we present experimental results on genome assembly using quantum annealers both for simulated data and the de novo genome assembly. To the best of our knowledge, this is the first experimental study of de novo genome assembly problems both for real and synthetic data on quantum annealing devices and quantum-inspired techniques.Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for  More than 40 years ago, the first DNA genome . Read mapping on a backbone of the reference genome is computationally more simple and allows detection of single- and oligonucleotide mutations, which are the major causes of human diseases8. However, the detection of genome rearrangements is a complicated task9. Read mapping algorithms used for the analysis of clinically important samples use local de novo assembly to correct mapping errors and reference mismatches10. De novo assembly is currently used in transcriptome and cancer analysis, as gene fusions and genome rearrangements are common causes of malignant tumours11. Decreasing the costs of sequencing makes whole-genome sequencing an irreplaceable part of personalized medicine and cancer treatment. The utility of sequencing technologies requires improved workflows with de novo assemblers to uncover significant genomic rearrangements in cancer and normal tissues.Existing approaches in sequencing read analysis are based on 12. Overlap discovery involves all-against-all, pair-wise read comparison, where one sets up the minimal number of shared nucleotides between two reads and an allowed number of mismatches. In the OLC graph, each read is represented by a vertex and an edge between two vertices indicates the overlap between corresponding reads. Then, finding the Hamiltonian path, i.e., the path that goes through all vertices and visits each vertex only once, allows reconstructing the original genome. This approach is widely used in assemblers  and becomes suitable for the single-molecule sequencing technologies16.Early generations of assembly tools are based on the overlap layout consensus (OLC) algorithm17. The idea is to construct a graph based on the fragmentation of reads down to smaller sequences called k-mers, where k is the length of subsequence. These k-mers are aligned using k-mer graph represents a certain k-mer, while edges correspond to the overlaps between the k-mers. Thus, each read is represented by the sequence of the connected vertices . To obtain the original genome sequence one needs to find the Eulerian path, i.e., the path that visits each edge exactly once, but is allowed to revisit any vertex. The comparison of the OLC and DBG approaches are discussed in more detail in Ref.15. As was mentioned above, the time of de novo assembling may be crucial for many applications. Possible improvements and speed-ups of the DBG approach, employing the Eulerian path, have been considered, whereas methods based on finding the Hamiltonian path in the OLC approach are less studied.It is well known that finding a Hamiltonian cycle belongs to the class of NP-complete computational problems, for which finding an efficient solution is very hard. That is why the other graph representation is applied to the analysis of the sequencing data. This approach is related to the concept of De Bruijn graphs (DBG)18 have a great potential to outperform existing technologies in various problems19, such as simulating complex systems20, machine learning21, and optimization22. Ongoing research are related to the question how quantum computers could be used for computational biology and bioinformatics23. One of the algorithms that can be realized using quantum computers is Grover’s search24, which can be used as a subroutine for sub-sequence alignment with a quadratic speed-up25. There is increased activity at the interface of machine learning and quantum computing in the computational biology domain27. Being of extreme interest from the viewpoint of obtaining polynomial and exponential computational speedups, the suggested quantum algorithms28 require both a significant number of qubits and quite low error rates, which are beyond the capabilities of existing noisy intermediate-scale quantum (NISQ) devices.Quantum computers are a new generation of devices that use quantum phenomena, such as superposition and entanglement, for solving computational tasks. It is believed that quantum computers31. However, the ability of realistic quantum annealing devices to demonstrate computation speedups is still a subject of ongoing research37. An interesting outcome of these debates is the appearance of a new generation of quantum-inspired  algorithms, which are essentially classical but appear as a result of analysing the role of quantum phenomena in solving computational tasks40. Results on the comparison between available quantum annealers and quantum-inspired algorithms on realistic optimization problems have been obtained40. We note that quantum annealing has been applied to various real-world tasks, including computational biology41, exploration of the conformational landscape of peptides and proteins42, and genome sequence alignment28.Although many different implementations and models of quantum computing are in development, one of the approaches, which is based on quantum annealing, deserves a special attention. This is due to the fact that the hardware for its implementation is available (it is produced by D-Wave System)de novo genome assembly problem within the framework of quantum annealing. On the one hand, the OLC approach is less sensitive to sequencing errors and repeats than the DBG approach which leads to the higher quality of the assembly. On the other hand, the main disadvantage of the OLC-based algorithms is their computational inefficiency15. Particularly, as we need to solve the NP-hard problem of finding a Hamiltonian path in the graph. Quantum computations have already shown their potential suitability for solving such problems. The above mentioned arguments motivate us to focus on the OLC formulation of the de novo genome assembly problem. The main step in our study is to map the genome assembly problem in the framework of OLC graphs to a quadratic unconstrained binary optimization (QUBO) problem, which can be then efficiently embedded in the quantum annealing architecture  is related to their potential in solving combinatorial optimization problems. It is widely discussed that the potential of quantum annealing is rooted in the quantum effects that allow us to efficiently explore the cost-function landscape in ways unavailable to classical methods. Therefore, the important stage is to map the problem of interest to a Hamiltonian, which maps the binary representation of a graph path into a corresponding energy value. The existing physical implementation of quantum annealing is the D-Wave processor, which can be described as Ising spin Hamiltonian. The Ising Hamiltonian can be transformed into a QUBO problem. Thus, we have to find the mapping to a problem that we would like to solve on the D-Wave quantum processor to the QUBO form. However, establishing correspondence between a problem of interest and the QUBO form may require additional overhead. In particular, in our case the transformation of the OLC graph to a QUBO problem requires the use of additional variables (see below).In addition, the D-Wave quantum processor has its native structure (the chimera structure). That is why after the formulation of the problem of interest in the QUBO form an additional stage of embedding problem in the native structure of the quantum device is required. So additional overhead in the number of physical qubits, which is related to the representation of logical variables by physical qubits of the processor (that takes into account the native structure), is required (see below).43, we reformulate the task of finding the Hamiltonian path in the OLC graph as a QUBO problem.Along the lines of Ref.E is set of edges consisting of pairs  with vth node at the ith step. Then, we assign each element N-vertex graph requires Let a directed OLC graph be given in the form mentclass2pt{minimM logical variables, where u, v) is included in the Hamiltonian path. Then the corresponding Hamiltonian should include the following two components:In general, Hamiltonian path mapping is suitable both for cyclic and acyclic directed graphs. However, it is often the case that the OLC graph contains no cycles. It is then possible to further simplify transformation and reduce the qubit overhead. Here, we demonstrate more compact mapping that requires only M variables, where M is the number of edges in the corresponding OLC-graph), the asymptotic computational speed-up versus classical algorithm is not exponential .The first and the second terms in Eq.  assure t31. Within a C16 Chimera graph, physical qubits are logically mapped into a 32. It allows obtaining a desired effective Hamiltonian by assigning several physical qubits of the processor to a single logical variable of the original Hamiltonian   2) are nde novo genome assembly using quantum and quantum-inspired annealers. As a figure of merit we use the time-to-solution (TTS), which is the total time required by the solver to find the optimal solution (ground state) at least once with a probability of 0.99. We first define Here we apply our method for the experimental realization of Then we define TTS it in the following way:38, which is based on the differential approach to simulating specific quantum processors called Coherent Ising Machine , compare the performance of the D-Wave quantum annealer with a software annealing simulator SimCIM. The choice of tools is motivated by their maturity in terms of quantum dimensionality and compatibility with the original formulation in terms of the optimization problem. The similar routine is realized with the use of quantum-inspired annealing. We test the suggested approach with the simulated data first with the D-Wave quantum annealer see Fig.  and compWe note that the D-Wave annealer shows an advantage in genome assembly for short-length sequences, while it cannot be applied for sequences of length 6 and more due to the fact that the decoherence time becomes comparable with the annealing time. What we observe is that the performance of the annealing system is dependent on the properties of input data. While the exhaustive investigation of the nature of D-Wave performance with respect to input data goes beyond the scope of our research, we consider the connectivity of the input graph as one of the critical factors. The D-Wave 2000Q processor is based on Chimera Topology with native physical connectivity of 6 basic qubit cells.During the experiments on the synthetic dataset, we were able to embed the problems with a maximum sequence of up to 10 nucleotides. This length corresponds to the fully connected graph with 8 nodes  and this is the maximum possible graph size, which can be embedded to the chimera lattice using clique embedding tool from DWave Ocean SDK. While Ocean SDK allows using other types of embedding  we observed that clique embedding demonstrates more stable results due to the deterministic nature of embedding in comparison to the minor-miner tool, which is intrinsically based on randomized heuristics contributing to larger deviations across experiments. However, no viable solution that could reconstruct the original sequence was found for sequences longer than 6.47 and trapped ions49 can be also used for the efficient implementation of quantum annealing and other quantum optimization algorithms. Specifically, the system of Rydberg atom arrays has been studied in the context of solving the maximum independent set problem47, which is NP-hard. For longer sequences, as we have demonstrated, it is possible to use quantum-inspired algorithms that are capable of solving more complex problems using classical hardware.In our work, we have demonstrated the possibility of solving the simplified bioinformatics problem of reconstructing genome sequences using quantum annealing hardware and quantum-inspired algorithms. We have implemented the experimental quantum-assisted assembly of We note that our work is a proof-of-principle demonstration of the possibility to use existing quantum devices for solving the genome assembly problem. The problem scale considered in this paper is still far from real sequences , genome contaminants (pieces of the genome not related to the subject of interest), polymer chain reaction artifacts, and others require additional post-processing steps. These problems are beyond the scope of our proof-of-principle demonstration and they should be considered in the future. Another complication comes from the fact that temperature and other noise effects play a significant role in the case of the use of realistic quantum devices. Thermal excitation and relaxation processes affect performance. Our further directions include optimization of the QUBO model for more compact spin representation and integration of error model into our algorithm. Solving these two issues can enable reconstruction of real sequences using the quantum approach.x-matrix, which acts on ith qubit. The problem Hamiltonian can be encoded to the following Ising Hamiltonian:z-matrices, and E is the set of edges. One can see that The beginning Hamiltonian of the D-Wave processor is a transverse magnetic field of the following form:Quantum annealing can be applied to any optimization problem that can be expressed in the QUBO form. The idea is then to reduce the problem of interest to the QUBO form.43 provides a method for QUBO/Ising formulations of many NP problems.The Ising Hamiltonian can be directly transformed to a quadratic unconstrained binary optimization (QUBO) problem. The following transformation can be applied for this purpose:SimCIM is an example of a quantum-inspired annealing algorithm, which works in an iterative manner. It can be used for sampling low-energy spin configurations in the classical Ising model. The algorithm treats each spin value Grinder50 to simulate raw reads from We use minimap2 package51. We run minimap2 with the predefined set of parameters ava-ont and miniasm14 to the same data as the benchmark assembler, which uses OLC graphs.We generate the raw reads with no sequencing errors and the length of each read is equal to 600 base pairs. We build the OLC graph using the pairwise alignment of the raw reads implemented in For experiments with quantum annealing, we use public access to D-Wave 2000Q via Leap SDK. We evaluate the impact of tunable parameters  on the final solution quality; however, no significant improvement was discovered against default values, so annealing time was set to 20 44. It allows splitting the original graph into 3 sub-parts. They are carefully selected so that only a single edge remains between them. The longest path is then calculated separately for each part and concatenated into a single path of the original graph. Each part is still large enough to be computed using the purely quantum mode, so we use the D-Wave hybrid computing mode — hybridSynthetic dataset graphs, which consist of reads no longer than 7 nucleotides (25 graph nodes), are small enough to fit into quantum annealer, so we can use DWIn order to evaluate the performance of the algorithm in a controlled setup, we generated several hundreds of random nucleotide sequences with variable length and performed corresponding transformations as shown in Fig. Note Added. Recently, we became aware of the work reporting studies of the quantum acceleration using gate-based and annealing-based quantum computing52.


Self-perceived health is a subjective health outcome that summarizes all the health conditions and is widely used in population health studies. Yet, despite its well-known relationship with survival, it is still unclear as to which health conditions are actually taken into account when making an individual assessment of one's own health. The aim of this paper is to assess the influence of four objective health conditions – IADLs, ADLs, chronic diseases, and depression – in predicting self-perceived health among Europeans by age group (50–64 and 65–79) and by sex.Classification trees , which pertains to the emerging Machine Learning techniques, were applied to predict self-perceived health according to the four abovementioned objective health conditions of European individuals in the sixth wave of the Survey of Health, Ageing and Retirement in Europe (SHARE) .The four variables present different degrees of relevance in establishing predictions of self-perceived health values by age and by sex. Before the age of 65, chronic diseases have the greatest importance, while IADL limitations are more important in the 65–79 age group. Likewise, ADL limitations are more important for women free of chronic diseases in the 50–64 age group; however, these differences disappear among women in the older group.There is an evident degree of interplay between the objective health indicators of chronic diseases, ADLs, IADLs, and depression when predicting self-perceived health with a high level of accuracy. This interplay implies that self-perceived health summarizes different health conditions depending on age. Gender differences are only evident for the younger age group, whereas construction of self-perceived is the same for women and men among the older group. Therefore, none of these four indicators on its own is able to totally substitute self-perceived health. •Self-perceived health constitutes a black box because of its subjective nature and the fact that it summarizes all the health conditions of an individual in a single indicator.•This is one of the first studies to apply predictive algorithms, as developed in machine learning, to an examination of population health.•Results in this study provide valuable insights into what self-perceived health actually encompasses.•Future work using self-perceived health will benefit from a much more accurate understanding of this health indicator. Moreover, the current diversity of health measures enables us to capture the multidimensionality of the population's health as defined by the Self-perceived health, therefore, constitutes a black box precisely because of its subjective nature and the fact that it summarizes all the health conditions of an individual in a single indicator. The subjective nature of this indicator lies, at least partially, in the influence that the context can have on the individual's response, as pointed out by The aim of this short communication is to assess the influence of objective health conditions, both physical  and mental (depression), in predicting responses to questions about self-perceived health among European women and men between the ages of 50 and 79. The health conditions that contribute to a greater predictive capacity of self-perceived health should be those that have the greatest influence on an individual's perception of health. For this purpose, classification trees employed in machine learning, namely the J48 algorithm , are applied to European individuals who participated in the sixth wave of the Survey of Health, Ageing and Retirement in Europe (SHARE) . This clThe working sample was divided into two different age groups (50–64 and 65–79) in order to account for the effect of age on the influence of objective health conditions on self-perception of health, with older individuals showing a more favorable health perception . The ageThe contribution is twofold: first, this is one of the first studies to apply predictive algorithms, as developed in machine learning, to an examination of population health; and, second, thanks to the exploitation of this particular methodology, the evaluation I undertake of the contribution of objective health situations to individual  perceptions of health provides valuable insights into what self-perceived health actually encompasses. This complements the recent research on the structure of this subjective health outcome by 2The data analyzed herein are taken from the sixth edition of the Survey of Health, Ageing and Retirement in Europe (SHARE). SHARE is a panel survey that is representative of the non-institutionalized population in Europe, aged 50 and over. It gathers information about multiple aspects of this population, including demographics, work, family, health, housing, etc . The int-Number of chronic diseases. This variable is the result of aggregating responses to the battery of questions as to whether the person interviewed has been diagnosed with any of the all possible chronic diseases included in the questionnaire . The final variable was: no chronic disease; one or more chronic diseases.-Instrumental activities of daily living (IADL). Participants were asked whether they had any difficulty doing each of the following everyday activities: doing work around the house or garden; leaving the house independently/accessing transportation; shopping for groceries; doing personal laundry; managing money; preparing a hot meal; taking medications; and making telephone calls. Individuals were required to exclude any difficulties expected to last less than three months. The final variable was: no limitations; being limited to perform one or more activities.-Activities of daily living (ADL): Participants were asked whether, “because of physical, mental, emotional, or memory problems”, they had any difficulty doing these activities : dressing (including putting on shoes and socks); eating (such as cutting up your food); using the toilet (including getting up and down); bathing and showering; getting in and out of bed; and walking across a room. The final variable was grouped as follows: no limitations; being limited to perform one or more activities.-Depression: This variable was measured using the EURO-D scale, developed and validated by the EURODEP Concerted Action Project . EURO-D -Self-perceived health: This variable was based on responses to the question ‘How is your health in general?’ . Following common practice , we grouThe working sample comprised all persons aged between 50 and 79 years old residing in the 17 European countries  participating in the sixth edition of SHARE who answered all the questions included in our analysis . All the variables taken into consideration to train the classification algorithms were dichotomized so as to facilitate the interpretation of the resulting classification trees. Previous trials employing just three categories for all the health outcomes other than self-perceived health had resulted in confusing classification trees and no meaningful improvements in their accuracy (less than 3 percentage points on average). The variables considered were the following:The classification algorithm selected was the J48 , an upda). Under k-fold cross-validation the data are randomly partitioned into k different subsets of approximately equal size. In the ith fold of the cross-validation procedure, the ith subset is used to test the performance of a model trained on the remaining k − 1 subsets. The average of the performance observed over all k folds allows us to estimate the performance of a model trained on the entire sample  of each of the models obtained using this algorithm with the values obtained from the random forest classification tree, an algorithm that fits an ensemble of decision tree models and calculates the average between all possible decision trees . The lat3If we examine the classification trees for women and men aged between 65 and 79  and mental (depression), in predicting responses about self-perceived health in European women and men aged between 50 and 79. The predictive capacity was assessed by means of classification trees based on the J48 algorithm, which belongs to the family of machine learning methods, and by using data from the sixth wave of the SHARE survey. The approach reported contributes to a better understanding of a health outcome that has been used to describe general population health profiles without our having a clear idea of what health conditions actually influence individual perceptions. The results complement and expand recent research on health situations associated with self-perceived health  by usingThe results reported herein confirm the high predictive capacity of self-perceived health based on four of the most widely used health indicators in the literature, namely chronic diseases, IADLs, ADLs and depression. However, differences are observed between the two age groups (50–64 and 65–79) in terms of the order of importance of each of these four variables in establishing predictions of self-perceived health values. Before the age of 65, chronic diseases are shown to have the greatest importance in predicting the self-perceived health of people in this age group, while among those over the age of 65, IADL limitations become more important. This shift in the influence attributable to different health situations seems to be in line with the effects of the disablement process proposed by The differences between the sexes, as regards the contribution of the four health indicators used in defining the classification trees, are found to be less notable in the older group. This would confirm the non-existence of a gendered pattern of response to the question on self-perceived health at least at older ages, as previously pointed out by 5All in all, this study has demonstrated the complementary nature of the four health indicators analyzed  in predicting self-perceived health with a high level of accuracy. This complementarity implies, however, that none of these four indicators on its own is able to substitute self-perceived health as a general indicator of health. This conclusion is strengthened by the fact that the predictive capacity of the four health indicators of self-perceived health has been shown to vary according to the age group analyzed, and even according to sex among those under the age of 65. Therefore, researchers should be aware of what self-perceived health actually encompasses when taking it as an indicator to capture differences and inequalities in health for the general population. Future research needs to explore whether this pattern of prediction differs across countries or education attainment, in line with the differences in health perception across European countries or education reported in earlier studies .Jordi Gumà: Conceptualization, Methodology, Data curation, Writing- Original draft preparation.http://www.share-project.org/fileadmin/pdf_documentation/SHARE_ethics_approvals.pdf.The University of Mannheim's internal review board reviewed and approved SHARE for wave 1 to 4. Ethics Council of the Max Planck Society conduct the ethics reviews for wave 4 onwards. Ethics approvals in each of SHARE-participating countries were obtained from the local ethics committees or institutional review boards. SHARE data is available for scientific community and may only be used for scientific research. The secondary data analysis of SHARE data, such in the present study, do not require further ethical approval. Details on SHARE ethical approval is available in FEDER/Spanish Ministry of Science, Innovation and University/Spanish Agency of Research and is part of the project “Prevention is better than cure when ageing is behind the door: interplay between social determinants of health in Spain (INTERSOC-HEALTH)” .This work was supported by the The authors report no conflict of interest.


Due to the possibilities in miniaturization and wearability, photoplethysmography (PPG) has recently gained a large interest not only for heart rate measurement, but also for estimating heart rate variability, which is derived from ECG by convention. The agreement between PPG and ECG-based HRV has been assessed in several studies, but the feasibility of PPG-based HRV estimation is still largely unknown for many conditions. In this study, we assess the feasibility of HRV estimation based on finger PPG during rest, mild physical exercise and mild mental stress. In addition, we compare different variants of signal processing methods including selection of fiducial point and outlier correction. Based on five minutes synchronous recordings of PPG and ECG from 15 healthy participants during each of these three conditions, the PPG-based HRV estimation was assessed for the SDNN and RMSSD parameters, calculated based on two different fiducial points (foot point and maximum slope), with and without outlier correction. The results show that HRV estimation based on finger PPG is feasible during rest and mild mental stress, but can give large errors during mild physical exercise. A good estimation is very dependent on outlier correction and fiducial point selection, and SDNN seems to be a more robust parameter compared to RMSSD for PPG-based HRV estimation. PPG is a method that measures the change in volume by using light. This method can be used to measure the pulsating dilatation of blood vessels, caused by the heart, by attaching a PPG sensor to the skin. The PPG sensor transmits a light signal which is reflected by or transmitted through the blood vessels. The reflected or transmitted light from the area covered by the PPG light source provides a pulsating signal, which is picked up by a photodiode. The pulsating component of the PPG signal is synchronous to the heartbeat but has a delay corresponding to the transit time of the blood from the heart to the point of measurement ,2. In thHeart rate variability (HRV) is related to the interaction between the sympathetic and the parasympathetic nervous system . ECG hasSeveral studies have demonstrated good performance in estimation of heart rate based on PPG, even during intensive exercise , but theThe signal processing of the PPG signal plays an important role in comparison to ECG-based HRV. In this study, we assess the feasibility of PPG-based HRV estimation during rest, mild exercise and mild mental stress. Our approach was to record finger PPG and ECG simultaneously from healthy volunteers during each of these conditions, calculate the most common time-domain HRV parameters based on both ECG and PPG, and assess the performance of PPG-derived HRV parameters based on statistical analysis. In addition, we evaluate different variants of signal processing for deriving the inter-beat interval time series used for calculating the HRV parameters, including the selection of fiducial point and outlier correction.This study aimed to assess the agreement between heart rate variability derived from finger PPG and ECG during rest, mild exercise and mild mental stress and comparing different signal processing methods.Two Shimmer3 sensor platforms , with built-in data loggers, were used to collect data from a PPG sensor and taking ECG measurements simultaneously.The Consensys Pro software  was used to extract the data and export it to a readable format. Consensys Base 6 was connected to transfer the data from the wireless Shimmer3 sensor platform to the Consensys Pro software.The PPG sensor used in this study contains a super bright green light-emitting diode (LED) and an ambient light sensor that detects the reflected light from the blood vessels. The sensor was connected to the Shimmer3 GSR+ sensor platform with a 3.5mm jack cable. The voltage created by the light sensor was read and converted by the Shimmer ADC to a 12-bit number that represents the PPG-signal in mV.The electrodes used for ECG measurement was the Q00A wet gel electrode from Ambu . The Shimmer3 ECG unit has an ECG front end which contains an electromagnetic interference (EMI) filter that reduces EMI, and a configurable gain. We used the default gain setting for these measurements (level 6). The Shimmer3 ECG unit also have a respiration demodulation function and a lead-off detection, but this was not used during this study. Both the PPG and ECG signals were sampled at 1kHz. The ECG signal from the LL (left leg)-RA (right arm) lead was used for the HRV analysis. The placement of the sensors and ECG electrodes is shown in Twenty-one healthy subjects participated in this study. A majority of them were male (18) and 3 of them were female. The average age of the participants was 26.3 years (SD = 6.2 years), the average height was 180.8 cm (SD = 9.6 cm) and the average weight was 74 kg (SD = 12.4 kg). All participants were informed and gave written consent before the test was initiated. During the test, the participants wore five electrodes to be used for ECG recording. The skin was disinfected with an alcohol swab before the electrodes were attached to ensure good conductivity. The electrodes were placed according to the five-lead Mason-Likar system with the V-lead at V1 . The ECGThe participants underwent three phases during the measurement. In the first phase, the participant sat relaxed in a chair and rested for five minutes during measurement. In phase two, the participant was asked to cycle with low intensity on an ergometer bike for five minutes during the measurement. In the final phase, the participant was asked to play a game designed to measure the signals during mental stress. To give the test subjects a controlled level of mild mental stress, the python-based program LARA was used . This isInitial inspection of the recordings revealed that saturation of the PPG signal would often occur, clipping the signal at around 2800 mV amplitude as shown in A Savitzky-Golay filtered  version of the signal was then differentiated in order to obtain the first derivative of the PPG signal (dPPG). The dPPG was then used to locate negative to positive zero-crossing points of the first derivative, representing PPG signal valleys. These locations were then filtered by excluding those having a too small subsequent PPG wave (the following dPPG peak less than 0.5 mV/ms). Further exclusion of false points was done by adaptive threshold-based filtering . Comparison of the current PPG peak to the previous and next peak was then done, excluding points where the PPG peak is lower than 75% of both the previous and next PPG peak, as these are more likely diastolic peaks.The filtered vector of PPG valleys was then used as locations of the PPG foot fiducial point, and the locations of the subsequent dPPG peak was used as the PPG max slope fiducial point . The vecThe ECG-based RR intervals were located by employing the Pan-Tompkins algorithm  using a The time-stamp of the recordings had occurrences of time steps far larger than that of the sampling rate along with signal distortion, and beats belonging to these were identified by detection of time step above 100 ms within a beat. For both the RR and IBI time-series, these beats were replaced by a linear interpolation between the points before and after.Missing detection or erroneous identification of fiducial points will often lead to outliers in the IBI time vector, which can possibly be identified and filtered automatically. In order to assess the importance of such filtering, an outlier correction filter similar to  was implBased on the IBI and RR vectors, the widely used HRV parameters SDNN  and RMSSD  were calculated. These parameters were calculated for each participant and every phase, based on the RR vectors and both the unfiltered and filtered IBI vectors. Agreement with ECG-based HRV in each phase was assessed by calculating the median absolute deviation (MAD), the median absolute relative deviation (MARD) and the root mean square error (RMSE) between PPG-based and ECG-based HRV over all subjects. Bland-Altman plots were also constructed for each comparison of HRV calculation. In addition, and for relevance to heart rate measurement, a comparison between the PPG-derived IBI and the ECG-derived RR intervals was done based on the averages within five-second intervals of each recording, presented as MAD, MARD and RMSE. These error measures were first calculated over all five-second intervals within each recording, and the median was then taken over all subjects.Informed consent has been obtained from all individuals included in this study.The research related to human use has been complied with all relevant national regulations, institutional policies and in accordance with the tenets of the Helsinki Declaration.The average heart rate within each period , shows tInitial inspections revealed that one session had missing ECG data and five sessions had a malfunctioning acquisition of PPG signals in all three phases, and had to be excluded from the analysis, resulting in 15 sessions with three complete phases used in the analysis. Visual inspection indicated that the signal quality of PPG was generally good in the resting and mental stress phases, but poor in the exercise phase , the PPG-based estimates of SDNN were more correct than the RMSSD estimates. Taking all cases into account, the best agreement for both SDNN and RMSSD was for Max slope based HRV estimation with outlier correction during the resting and mental stress phases.The agreement between the R-to-R (RR) intervals derived from ECG and the inter-beat intervals (IBI) derived from the PPG is provided in Our results show that HRV estimation based on PPG is strongly dependent on the type of activity and the method of signal processing. The maximum slope as a fiducial point performed better than the foot point of the PPG signal.Outliers due to artifacts gave rise to large errors if uncorrected before HRV calculation. When using the maximum slope as fiducial point together with outlier correction, good agreement was found for both SDNN and RMSSD during the resting and mental stress periods.As shown in The large overestimation of HRV during exercise was due to movement artifacts hampering the signal quality by including waves that are difficult to discriminate from the true waves of pulsation. It has been shown that the combined use of an accelerometer signal together with PPG can improve heart rate estimation , but thiAs demonstrated in We used a finger placement of the PPG sensor rather than the wrist even though wrist-worn devices are most used by commercial wearable manufacturers. However, some commercial manufacturers have found it convenient to use a ring with a build-in PPG-sensor or a finger cuff with a sensor to connect with a smartphone ,23. SomeThere were no restrictions on how much the participants were allowed to move during this study. This means that unnecessary disturbance may have been introduced to the PPG measurements. For further research on this topic, the earlobe sensor would be interesting to assess for HRV estimation. The earlobe sensor is supposed to be less prone to motion artifacts and may have lower variability in the skin-sensor interface.We had the technical issue of signal saturation from the PPG sensor and due to the PPG sensor signal cutoff, it was not possible to assess the PPG-based HRV estimation using the PPG peaks as fiducial points. However, other studies have found the valley or maximum slope points to be more accurate compared to the peak point in HRV estimation ,27, suggIt is possible that further improvement of the PPG signal processing and fiducial point detection could improve the HRV estimation, but we believe that our main findings stand pertinent nevertheless: That finger PPG can provide a good estimation of HRV during relaxation and mental stress, that movement artifacts during exercise can cause large errors, and that outlier correction is essential. We are not able to tell to which extent our findings are relevant for PPG sensors in general or the particular sensor used in this study (Shimmer 3 GSR+ unit), as both optics and signal conditioning may vary from device to device.Measurement of heart rate by PPG during exercise is already challenging due to motion artifacts, and advanced signal processing is needed to provide good estimates ,28, possOur results clearly show that finger PPG-based HRV estimation is feasible during relaxation and mild mental stress, but can have large errors even during mild physical exercise. The HRV estimation is very sensitive to outliers in the time-series of interbeat intervals and produces large errors when uncorrected. The maximum slope point of the PPG signal may be the most optimal fiducial point for HRV estimation. SDNN seems to be more robust for PPG-based HRV estimation compared to RMSSD.


The uterine electromyogram, also called electrohysterogram (EHG), is the electrical signal generated by uterine contractile activity. The EHG has been considered an expanding technique for pregnancy monitoring and preterm risk evaluation. Data were collected on the abdominal surface. It has been speculated the effect of the placenta location on the characteristics of the EHG. In this work, a preliminary exploration method is proposed using the average spectra of Alvarez waves contractions of subjects with anterior and non-anterior placental position as a basis for the triple-dispersion Cole model that provides a best fit for these two cases. This leads to the uterine impedance estimation for these two study cases. Non-linear least square fitting (NLSF) was applied for this modelling process, which produces electric circuit fractional models’ representations. A triple-dispersion Cole-impedance model was used to obtain the uterine impedance curve in a frequency band between 0.1 and 1 Hz. A proposal for the interpretation relating the model parameters and the placental influence on the myometrial contractile action is provided. This is the first report regarding in silico estimation of the uterine impedance for cases involving anterior or non-anterior placental positions. The EHG has been used as a modern tool for pregnancy monitoring and preterm risk evaluation ,2. It haFractional calculus is a powerful tool for modelling phenomena in science and engineering. Although its history dates back as far as integer-order calculus, its progress over the last thirty years has been enormous and has become the object of great interest of not only of mathematicians but also other researchers in science and technology ,20,21,22eristics ,33,34,35eristics ; investieristics ; assessieristics ; modellieristics ,40,41; aC is the capacitance, measured in Farad/On the other hand, for describing the fractional character of these fractional calculus-depending models, it is natural to consider the CPE described by the current-voltage relationship in the following differential equation:rivative . For desrivative :(2)DGLαvIn this study, the placental position influence on the EHG spectral parameters will be investigated using a preliminary exploratory methodology. The anterior placenta is positioned at the front wall of the uterus and is therefore in the projection of the myometrium and the acquisition electrodes. This placenta position has the potential to influence the EHG characteristics. The other placenta positions, herein referred to as non-anterior, are not in the electrode’s projection. The main goal is to obtain the electrical impedance fractional estimation in silico model of the uterine tissue using non-invasively obtained data. Considering that anterior placenta stands in the alignment of the electrodes and the myometrium, its effect on the impedance model is concurrently studied. A tentative interpretation of the results is provided. To the best of the authors’ knowledge, this is the first study using the mentioned methodology for the uterine impedance estimation modelling.The used data were provided by the Iceland Uterine Electromyography database , comprisA fractional-order transfer function is obtained from In this work, a nonlinear least square fitting (NLSF) procedure based on the trust-region-reflective approach was performed to obtain parameters of the model in Fractional circuits have been used in biomedicine and biology for modelling tissue impedance ,44,54. Tlsqnonlin for the implementation of this NLSF process based on [lsqnonlin function is specified by the goal function as follows:x is the vector of parameters , with coefficients The parameters to be obtained in Equation (3) are real values providing best fit for anterior and non-anterior placental position cases. These parameters were extracted through an algorithm involving the MATLAB function based on ,56. The F filter transfer function is represented in The Moreover, NLSF processing needs initial points, namely lower and upper bounds for each parameter in Equation (4). All lower bounds for G in Equation (6) is also obtained, which determines the good quality of the approximation of the estimate function G to the spectrum.The optimal values of parameters H(s) poles are located on the left-half plane, as shown in As a result of the optimization fitting procedure applied to the model given by expression (3), the values in The time constants for the three Cole dispersion models are obtained by:Using the classic formulation, the cut-off frequency is obtained:τ1 values in both placenta position cases represent a long-range process component of more than half an hour, corresponding to very low cut-off frequencies.τ1 have been excluded. The real and imaginary impedance axes do not represent the physical resistive or reactive components of the myometrial or myometrial plus placental tissue. The herein presented method is based on a spectral output, from which the obtained physical impedance values cannot be achieved. However, the impedance curve waveshape remains the same. Rescaling the impedance axes to physical values is possible if some physical impedance points are known. The 0.45-Hz cut-off frequency in the non-anterior placenta case is associated with a sharp impedance curve variation if compared with the corresponding 0.37-Hz cut-off frequency in the anterior placental case. This indicates that the time constant τ2 has more impact in the impedance variation for the anterior placental case.The obtained fractional circuit accurately represented the original spectral estimation for the anterior and non-anterior placental cases using only a triple-dispersion Cole model. This emphasizes fractional systems as an efficient tool to model complex electrophysiological phenomena, in this case, the uterine tissue impedance. It is also indicative of the potential fractional nature of the electrical characteristics of the uterine tissue. The presented study estimated, non-invasively, uterine tissue impedance using EHG data collected in the abdominal surface and projected to the spectral domain. The elegancy of the method has, however, the drawback of not being able to estimate the physical values of the tissue impedance. What is obtained is a Nyquist plot of the uterine impedance model. Nevertheless, a scaling to realistic impedance values is possible if actual resistance and reactance value pairs are known, via, for instance, in vitro or in vivo experiments.During early human pregnancy, the trophoblast, an embryonic structure that will originate the placenta, invades the decidualized endometrium up to the inner third of the myometrium. It migrates in a retrograde direction along the spiral arteries, transforming them into large-diameter conduit vessels of low resistance . UteroplThe mentioned remodelling could be in favour of a decreased myometrial impedance in cases where the placenta is anterior as a result of large uteroplacental vessels implantation, allowing increased placental blood flow . This isRegarding the intriguing increase in the frequency for the peak impedance value  in the aLower energy levels for anterior placenta, as reported in Low energy levels identified in our study may also be a result of blocked propagation of electrical activity from the cells of the non-placental region to the placental region  presumabOur results show different myometrium frequency dependent impedance curves for the anterior placenta compared to non-anterior placenta case. In view of these results, it would be possible to hypothesize that:Our results are in accordance with Kavšek et al. , who alsContrary to the study of Kavšek et al. and the herein presented one, Dermott et al.  reportedThe field of vegetal and animal fractional tissue modelling has presented interesting outcomes. Likewise, fractional calculus has the potential to explore and model myometrium electrophysiological phenomena. This could be an important contribution in areas such as pregnancy monitoring, preterm risk evaluation, and uterine electrophysiological research.


The electro-mechanical impedance (EMI) technique has been applied successfully to detect minor damage in engineering structures including reinforced concrete (RC). However, in the presence of temperature variations, it can cause false alarms in structural health monitoring (SHM) applications. This paper has developed an innovative approach that integrates the EMI methodology with multilevel hierarchical machine learning techniques and the use of fiber Bragg grating (FBG) temperature and strain sensors to evaluate the mechanical performance of RC beams strengthened with near surface mounted (NSM)-fiber reinforced polymer (FRP) under sustained load and varied temperatures. This problem is a real challenge since the bond behavior at the concrete–FRP interface plays a key role in the performance of this type of structure, and additionally, its failure occurs in a brittle and sudden way. The method was validated in a specimen tested over a period of 1.5 years under different conditions of sustained load and temperature. The analysis of the experimental results in an especially complex problem with the proposed approach demonstrated its effectiveness as an SHM method in a combined EMI–FBG framework. Effective strengthening techniques, such as externally bonded reinforcement (EBR) or near-surface mounted (NSM) using FRP materials, have been used in the last decade to increase the load carrying capacity of reinforced concrete (RC) structures. The NSM technique yields better bond performance and other potential advantages such as a better protection of FRP against external actions and minimal changes in the aesthetics of the structural elements ,2,3.The flexural and shear behaviors of RC beams strengthened with NSM-FRP under static loading conditions have been widely studied in the literature. However, although several studies have been performed regarding the combined effects of sustained load and temperature on the bond response of NSM-CFRP laminates in concrete elements ,5,6,7, sFurthermore, considering the uncertainty regarding the failure mode of this type of structure and the high probability of the occurrence of brittle and sudden failure, a structural health monitoring (SHM) methodology should also be implemented to predict any deterioration in the structure at its earliest stages and its evolution. Continuous measurement of strain represents an important part of SHM systems. Measured strains provide valuable information about the integrity of a structure. Fiber Bragg grating (FBG) optical sensors, unlike conventional electric strain gauges, are robust enough to sustain harsh working conditions and are immune to noise. Although damage modifies the load carrying capacity of a structure and creates modified strains, the strain variations due to the incipient damage are difficult to determine. The use of a lead zirconate titanate (PZT)-based electromechanical impedance (EMI) technique is more suitable and reliable for identifying incipient damage ,9. HowevMachine learning (ML) approaches are an interesting alternative way to detect hidden patterns in monitored data, and therefore, to separate the baseline from any anomalies experienced by the structure, either due to mechanical deterioration or change in temperature. This kind of technique might identify complex patterns related to different stages of the tested structure. The most common supervised machine learning algorithms are neural networks ,17, suppIn contrast, in unsupervised ML algorithms, the response of the problem is unknown. Clustering techniques are widely used in many practical applications for dimensional reduction ,24,25 anThis paper proposes a damage detection approach for NSM-FRP strengthened RC specimens subjected to sustained loading and variable temperature, based on the combined use of the PZT-EMI technique, FBG sensors and data processing based on multilevel clustering analysis. A concrete specimen strengthened with the NSM-FRP technique was subjected to different levels of sustained load for various time periods and at different temperatures during a test campaign of almost two years. The strain and temperature were continuously measured using FBG sensors. In the same way, after each sustained loading period or important temperature variation, an EMI test was performed with different PZT sensors located at different areas of the beam. FBG sensors and electromechanical impedance in conjunction with multilevel ML techniques have been employed independently in the past. We think that the combined use of FBG and PZT sensors in conjunction with clustering ML results in operational benefits for the monitoring of a problem in which the effects due to mechanical damage and temperature variations are coupled.Clustering analysis captures the intrinsic nature of a data set by making it possible to classify and categorize data in different groups according to their similarity. Within the different categories of clustering algorithms, hierarchical and k-means are the two most used types of classification ,27. K-meHierarchical clustering is one of the most commonly used methods for clustering data. By using this algorithm, the data set is divided into different clusters by iteratively merging or splitting clusters based on a dendrogram. Clustering algorithms provide information about the data to be classified in a compact and graphical way. They can be agglomerative or divisive depending on the procedure used to create the dendrogram. Agglomerative clustering follows a bottom-up strategy, in which, each data point is initially assumed to be a cluster and then it iteratively merges the two most similar clusters in terms of an objective function until the final dendrogram is obtained. By contrast, divisive clustering follows the opposite approach. All data points are considered initially as one cluster and then, iteratively, the selected cluster is partitioned into two new subclusters.An agglomerative methodology is computationally more advantageous and more frequently applied. As this approach involves merging the two most similar clusters at each step, the choice of a suitable similarity measure or distance function is important for the final result. Different alternatives are possible, such as single linkage (SL), complete linkage (CL) and all-pairs linkage (APL) clustering.As SL and CL are sensitive to noise and outliers, APL has been used in this study because of its higher robustness.K-means clustering is an unsupervised machine learning algorithm that groups clusters, sample points, or observations with a certain likeness to reveal hidden patterns. In this algorithm, the number of clusters must be defined a priori by the user. Then, an initial pattern of K clusters is randomly selected and each sample point is allocated to one of the produced clusters, using its minimum Euclidean distance from the center of that cluster as a reference. This process is repeated iteratively by updating the centroid of each cluster and the observations allocated in it, until the error is minimized and a suitable number of clusters is obtained. n is the number of frequency points in the impedance spectrum.In this work, to apply k-means clustering, the 3rd order moments of the real part of the measured impedance responses have been chosen as the characteristic feature to process the data set.In the EMI technique, PZT transducers bonded to the structure using high strength epoxy are electrically excited with an impedance analyzer in a user-defined frequency range for measuring the electromechanical admittance (inverse of the impedance). This admittance (Y), comprising a real part termed conductance (G) and an imaginary part termed susceptance (B), is captured in the form of signatures with respect to the exciting frequency operating in sweep mode and is directly related to the mechanical impedance of the structure . This meIf we place PZT sensors in different zones of the specimen to be analyzed, the impedance measurements captured from each sensor at different stages will serve to identify the anomalies experienced by the specimen near the sensors. These anomalies can be provided by the progressive deterioration of the structure but also by the environmental variability and the identification of each of these would be desirable. The application of a clustering strategy, either using hierarchical or k-means or both jointly, might be extremely useful for solving this problem because of its capacity to abstract valuable statistics from experimental data archives based on impedance in an unsupervised training framework. Clustering algorithms might partition data points according to the defined similarity, and therefore, would be useful for the classification of the data across all loading stages.The experimental program consisted of the study of the behavior of a RC beam strengthened with an NSM-FRP sheet that was subjected to different levels of sustained load in conjunction with different temperature levels. The study was conducted over a period of more than 1.5 years. The following subsections outline the details of the beam, the experimental protocol, as well as the instrumentation used during the different tests. One 120 mm × 150 mm RC beam was used to perform the experimental program. The geometric dimensions and the reinforcement layout in the section are illustrated in The beam was subjected to sustained load in four-point bending  and to tThe applied load was controlled by the weight of the materials put on the custom-made loading frame. The midspan deflection was recorded by a linear variable differential transformer (LVDT) and an electrical resistance strain gauge was installed to measure the compression strain at the midspan.B is the Bragg wavelength, neff is the effective refractive index, and Λ is the Bragg grating period. The FBG sensor consists of a periodic modulation of the refractive index along a certain length of the optical fiber, which is known as grating. When a FBG sensor is subjected to an axial strain or temperature change, the peak wavelength shifts proportionally to the variations in these two parameters, which means that the FBG sensor can be utilized as a temperature or strain-sensing unit. The performance along the FRP sheet was monitored by three FBG sensors, FBG1, FBG2, and FBG3 glued to the FRP laminate . The senConsidering that some temperature variations will occur in our experiment, an os4100 FBG sensor from Micron Optics , FBG4 sensor in The main goal of this work was to study the performance of the NSM-FRP RC beam under different conditions of sustained load and temperature. Hence, the change in the impedance across the different stages of the beam was also used. Impedances were captured from PZT patches bonded to the concrete tensile surface and to the FRP sheet; 61 mm × 35 mm × 0.5 mm and 16 mm × 13 mm × 0.5 mm PZT patches were used . The terAccording to An epoxy adhesive was used to bond PZT and FBG sensors to the specimen.To investigate the influence of the mechanism of the action of sustained load and temperature variations on the damage characteristics of the strengthened RC beam, the beam was experimentally tested for more than 1.5 years under different conditions of load and temperature, as shown in In general, except for the last loading stages, the methodology was as follows: (a) execution of one or several sustained load tests under the same predetermined load level and considering different durations; (b) unloading the specimen; (c) heating the specimen and maintenance of that temperature for 1–3 days; (d) removal of the heaters so that the beam reached room temperature. The beam stayed under room temperature and without loading for 1–3 days; (e) after step (d), the beam was subjected to a new sustained load test and the abovementioned procedure was repeated.The values of the applied sustained vertical load were 8, 9.3, 13.7, 17.7, and 19.6 kN. As mentioned previously, the first three levels correspond to the cracking load plus 15%, 35%, and 100%, respectively, the fourth level is associated with the steel reinforcement yielding, and finally, at the fifth level, because of the high level of yielding reached in the steel reinforcement, any new increment in internal tensile force was practically supported by the FRP reinforcement.The differences between impedance spectra provide a visual qualitative assessment of the variations between tests. Different damage metrics can be used to compare the quantitative variations between different frequency spectra based on the impedance. These damage metrics are statistical measures that allow us to identify deviations between two compared data sets associated with two states of the structure. Commonly used damage metrics include the root mean square deviation (RMSD), the mean absolute percentage deviation (MAPD), and the correlation coefficient deviation (CCD). In this work, the RMSD coefficient was used and it was computed between two consecutive stages as :(3)RMSD, a damage index is obtained for each sensor and test. k and Σk can be those defined from the initial healthy state or any other that might be appropriate. In Equations (4) and (5), the clusters taken as the baseline to compute µReadings from the FBGs, such as those shown in The impedance signatures were acquired only after each loading/temperature stage was completed and the specimen was unloaded. The PZT patches were interrogated at a frequency range of 10 to 100 kHz in steps of 12.5 Hz.The real part of the impedance is clearly more sensitive to the changes in impedance signatures; therefore, it was used in the proposed technique. Impedance signatures shift in magnitude and frequency as the temperature changes and damage increases. Furthermore, changes associated with a temperature variation (heating in test 12) can be confused with damage (test 35), resulting in the detection of a false positive damage.The RMSD values calculated according to Equation (3) from the real part of the impedance signatures for all PZT sensors are shown in In accordance with The results derived from hierarchical clustering can be visualized as a dendrogram. Dendrograms show the hierarchical relationship between tests. The first conclusion from Based on To get a deeper understanding of the results, an additional second level analysis was performed that considered only those tests under applied load, i.e., the heating and cooling tests were filtered in this second analysis. When k-means clustering is performed, the damage indicator shown in Equations (4) and (5) is computed for all observations. To confirm the conclusions derived from In this study, a clustering unsupervised machine learning system for SHM based on FBG and PZT measurements has been developed. Its performance was evaluated to identify minor damage by using the EMI method in the presence of sustained load and variable temperature. In a real scenario, the temperature variation can conceal real damage and it can also indicate false damage. The complementary nature of FBG and PZT smart sensors has been demonstrated to be key for developing a comprehensive SHM system applicable to a complex structural system in variable environmental conditions. The combination of multilevel hierarchical and k-means clustering techniques together with FBG measurements were used to provide a promising methodology for practical SHM applications.Even though the method was applied in RC beams strengthened with the NSM-FRP technique, it is an effective and original contribution to any SHM system based on EMI. It allows us to address temperature variations and mechanical deterioration in a direct way, with low computational complexity, and without using any reference baseline signatures measured at different temperatures such as is done in the usual temperature variation compensation techniques. The standard temperature compensation techniques are applicable in a lab framework; however, their application on real structures is more limited because of the lack of reference patterns to implement the compensation. With the proposed method, the analysis is performed in a direct way using the support of FBG measurements and unsupervised machine learning techniques.Despite the promising results, future work should assess the proposed approach in more depth when it is applied to more specimens considering other types of loads, such as fatigue loads and a narrower range of temperature variation. Additionally, the analysis of the performance of this method with other kinds of strengthening, such as EBR, should be carried out.