Machine Learning Algorithms for Classification of Microcirculation Images from Septic and Non-Septic Patients

Sepsis is a life-threatening disease and one of the major causes of death in hospitals. Imaging of microcirculatory dysfunction is a promising approach for automated diagnosis of sepsis. We report a machine learning classifier capable of distinguishing non-septic and septic images from dark field microcirculation videos of patients. The classifier achieves an accuracy of 89.45%. The area under the receiver operating characteristics of the classifier was 0.92, the precision was 0.92 and the recall was 0.84. Codes representing the learned feature space of trained classifier were visualized using t-SNE embedding and were separable and distinguished between images from critically ill and non-septic patients. Using an unsupervised convolutional autoencoder, independent of the clinical diagnosis, we also report clustering of learned features from a compressed representation associated with healthy images and those with microcirculatory dysfunction. The feature space used by our trained classifier to distinguish between images from septic and non-septic patients has potential diagnostic application.Comment: Accepted for publication at 2018 IEEE International Conference on Machine Learning and Applications (IEEE ICMLA

Kudede perfusioon ja metabolism intra-abdominaalse hüpertensiooniga patsientidel

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Eestis vajab kõrgeima astme intensiivravi peaaegu 10 000 patsienti aastas. Ligi kolmandikul neist esineb kõhuõõnesisese rõhu tõus, mis võib põhjustada kõhuõõne organite funktsioonihäireid ja on seeläbi seotud suurenenud suremusega. Tõusnud kõhuõõnesisene rõhk jaotatakse nelja-astmelisel skaalal: I 12-15 mmHg, II 16-20 mmHg, III 21-25 mmHg; IV üle 25 mmHg. Halvimal juhul, s.o kõhukoopasisese rõhu tõusul üle 20 mmHg võib kujuneda eluohtlik kõhuõõnesisene kompaartmentsündroom. Sel juhul on ravivõtted tavapraktikas üheselt mõistetavad – kiired ja agressiivsed. I ja II astme kõhuõõnesisese rõhu tõusu ravi on aga vastuoluline. Olemasolevad ravisoovitused ei anna täpseid juhiseid selle kohta, kas mõõdukas kõhukoopasisese rõhu tõus vajab kohest ravi. Antud töö eesmärk oli selgitada, kas I ja II astme kõhuõõnesisese rõhu tõus põhjustab tavapäraste jälgimismeetoditega mittetuvastatavaid muutusi kudede verevarustuses ja ainevahetuses. Verevarustus- ja ainevahetushäirete ilmnemine oleks oluline argument sündroomi raviks juba selle varajases staadiumis. Verevoolu muutuste hindamiseks kasutasime videomikroskoopi, millega uurisime patsientide keelealust veresoonestikku. Varasemad uuringud on näidanud, et selle piirkonna veresooned käituvad sarnaselt seedetrakti (mao ja soolestiku) veresoonestikuga ning seega peegeldavad keelealuse piirkonna muutused seedetrakti muutusi. Lisaks hindasime mikrodialüüsi metoodika abil ainevahetust kõhusirglihases. 37 haigel tehtud uuringute tulemusena leidsime, et kõhuõõnesisese rõhu tõus ei mõjuta oluliselt keelealuse piikonna verevarustust intensiivravi haigetel, kes on saanud eelnevalt vedelikravi. Küll aga oli keelealune verevarustus halvenenud kirurgilistel haigetel, kes olid plaanilise operatsiooni eelselt söömata-joomata. Kõhu sirglihase ainevahetuse hindamisel selgus, et I ja II astme kõhuõõnesisese rõhu tõus põhjustab hapnikuvaeguses tekkivate lõpp-produktide kuhjumist. See peegeldab verevarustuse olulist häiret. Kokkuvõttes rõhutavad töö tulemused, et vaatamata selgelt identifitseeritavate kliiniliste sümptomite puudumisele põhjustab kõhukoopa sisese rõhu mõõdukas tõus juba koekahjustust ja seetõttu ei tohi I ja II astme kõhuõõnesisese rõhu tõusu jätta ravita.Approximately 10000 patients are hospitalised to intensive care unit every year in Estonia. One third of them develop elevated intra-abdominal pressure (IAP) i.e. intra-abdominal hypertension (IAH). IAH can lead to severe abdominal organ’s dysfunction and is therefore a reason for elevated mortality. According to the severity, IAH is graded into four levels. Grade I refers to IAP levels from 12 to 15 mmHg, Grade II 16 to 20, Grade III 21 to 25, and Grade IV above 25 mmHg, respectively. The most severe form of IAH (IAP over 20 mmHg) is life-threatening abdominal compartment syndrome (ACS). Treatment of ACS is self-evident – fast and aggressive. Consequences of grade I and II IAH are not uniformly understood and the treatment recommendations are either absent or un-precisely defined. The main aim of present study was to investigate whether grade I and II IAH causes alterations in tissue perfusion and metabolism which are not detectable with conventional methods. Early treatment of mild to moderate IAH would be necessary if tissue perfusion and metabolism are deteriorated. Tissue perfusion was evaluated in sublingual area with videomicroscope. Several researches have previously shown that gastrointestinal and sublingual region microcirculation reacts similarly and that sublingual changes describe the situation in gastrointestinal region. For tissue metabolism evaluation we used microdialysis in the abdominal rectus muscle. Altogether 37 patients we included. Main finding of our work was that grade I or II IAH does not influence sublingual microcirculation in previously fluid-resuscitated critically ill patients. But the microcirculation was significantly altered in surgical patients, who were not allowed to eat-drink prior the elective surgery. The main finding of microdialysis study was the prevalence of anaerobic metabolism in RAM tissue during grade I and II IAH. This indicates to possible tissue hypoperfusion. In conclusion, the results of present work accentuate, that the tissue metabolism is severely altered during grade I and II IAH, despite the lack of clearly identified clinical symptoms and therefore IAH cannot be ignored in critically ill patients

Early microcirculatory dysfunction following traumatic haemorrhage

Traumatic haemorrhagic shock (THS) is the most frequent cause of preventable death after severe injury. Shock is characterised by inadequate provision of oxygen and substrates to tissues in relation to their requirements, and it is within the microcirculation that this process is regulated. Investigation of the microcirculation is therefore key to understanding the pathological processes following THS. In Part I, some mechanisms of microcirculatory dysfunction following trauma are presented. Endotheliopathy of trauma is associated with poor microcirculatory flow, and occurs within minutes of injury. It is also associated with higher levels of circulating cell-free DNA (cfDNA), supporting the hypothesis that cfDNA is an aetiological factor in this pathological response. Both endotheliopathy and elevated cfDNA and are related to poor clinical outcomes. In Part II, clinical implications of microcirculatory monitoring are discussed for patients in the early phase following THS. It is safe and feasible to monitor the microcirculation following THS, and a novel point-of-care grading system has performed well, suggesting that targeted fluid resuscitation towards microcirculatory flow after THS may be possible. The optimal fluid strategy in this context is unknown, but physical properties (e.g. oncotic potential and viscosity) as well as endothelial restorative properties appear to be as important as oxygen-carrying capacity. Potential therapeutic interventions aimed at microcirculatory and endothelial resuscitation open intriguing possibilities for improving outcomes after THS

Fast widefield techniques for fluorescence and phase endomicroscopy

Thesis (Ph.D.)--Boston UniversityEndomicroscopy is a recent development in biomedical optics which gives researchers and physicians microscope-resolution views of intact tissue to complement macroscopic visualization during endoscopy screening. This thesis presents HiLo endomicroscopy and oblique back-illumination endomicroscopy, fast widefield imaging techniques with fluorescence and phase contrast, respectively. Fluorescence imaging in thick tissue is often hampered by strong out-of-focus background signal. Laser scanning confocal endomicroscopy has been developed for optically-sectioned imaging free from background, but reliance on mechanical scanning fundamentally limits the frame rate and represents significant complexity and expense. HiLo is a fast, simple, widefield fluorescence imaging technique which rejects out-of-focus background signal without the need for scanning. It works by acquiring two images of the sample under uniform and structured illumination and synthesizing an optically sectioned result with real-time image processing. Oblique back-illumination microscopy (OBM) is a label-free technique which allows, for the first time, phase gradient imaging of sub-surface morphology in thick scattering tissue with a reflection geometry. OBM works by back-illuminating the sample with the oblique diffuse reflectance from light delivered via off-axis optical fibers. The use of two diametrically opposed illumination fibers allows simultaneous and independent measurement of phase gradients and absorption contrast. Video-rate single-exposure operation using wavelength multiplexing is demonstrated

Valor pronóstico del índice de saturación tisular de oxígeno (rso2) como expresión de la oxigenación tisular en pacientes con sepsis secundaria a neumonia adquirida en la comunidad.

Introducció: la pneumònia adquirida a la comunitat és una infecció alveolar que es desenvolupa en pacients que es troben en l’àmbit comunitari. Tot i el avenços, segueix representant una important causa de morbimortalitat al món. És important trobar la forma de detectar de forma precoç el grup de pacients que presenta pitjor pronòstic. En aquest context, la nostra investigació ha estudiat l’oxigenació tissular com un indicador indirecte de la microcirculació que pot servir per detectar de forma precoç pacients amb risc de presentar complicacions. Mètode: es van incloure pacient que ingressaven a UCI amb diagnòstic de pneumònia comunitària i es van realitzar determinació del índex de saturació tissular d’oxigen (rSO2) mitjançant tecnologia d’espectroscopia propera al infraroig. Es va determinar l’associació d’aquesta variable amb altres variables hemodinàmiques clàssiques i el valor predictiu de les variables per mortalitat. Resultats: la presència de rSO2 baix es va associar a major mortalitat en tots els estudis. Aquesta variable va demostrar major poder predictiu per a mortalitat que les extretes de la realització d’un test d’oclusió vascular (AUROC 0.790, IC 95% 0.637-0.943, p=0.004). La presència de rSO2 baix a d’ingrés i després de 24 hores de tractament van ser les úniques variables associades de forma independent a mortalitat (HR 8.99, IC 95% 1.05-76.8, p=0,045 i HR 13.18, IC 95% 1.52-113.6, p=0.019, respectivament). Conclusions: la determinació del índex de saturació tissular d’oxigen pot ajudar a reconèixer pacients amb sepsis d’origen respiratori amb major gravetat de forma més precoç que altres variables hemodinàmiques.Introducción: La neumonía adquirida en la comunidad es una infección alveolar que se desarrolla en pacientes que se encuentran en el ámbito comunitario. A pesar de los avances, sigue siendo una importante causa de morbimortalidad en el mundo. Es importante encontrar la forma de detectar de forma precoz el grupo de pacientes que presenta peor pronóstico. En este contexto, nuestra investigación ha estudiado la oxigenación tisular como un indicador indirecto de la microcirculación que puede servir para detectar de forma precoz pacientes con riesgo de presentar complicaciones. Método: se incluyeron pacientes que ingresaron en UCI con diagnóstico de neumonía comunitaria y se realizaron determinaciones del índice de saturación tisular de oxígeno (rSO2) mediante tecnología de espectroscopia cercana al infrarrojo. Se determinó la asociación de esta variable con otras variables hemodinámicas clásicas y el valor predictivo de las variables para mortalidad. Resultados: la presencia de un rSO2 bajo se asoció a mayor mortalidad en todos los estudios. Esta variable demostró mayor poder predictivo para mortalidad que las extraídas de la realización de un test de oclusión vascular (AUROC 0.790, IC 95% 0.637-0.943, p=0.004). La presencia de rSO2 bajo al ingreso y tras 24horas de tratamiento fueron las únicas variables asociadas de forma independiente a mortalidad (HR 8.99, IC 95% 1.05-76.8, p=0,045 y HR 13.18, IC 95% 1.52-113.6, p=0.019, respectivamente). Conclusiones: la determinación del rSO2 puede ayudar a reconocer pacientes con sepsis de origen respiratorio de mayor gravedad de forma más temprana que otras variables hemodinámicas.Introduction: community-acquired pneumonia is an alveolar infection. Despite progress it still represents an important cause of morbidity and mortality in the world. It is important to find a way to early detect the group of patients that presents worse prognostic. In this context, our investigation has evaluated tisular oxigenation as an indirect indicator of microcirculation’s state which can early detect patients at risk of presenting complications. Methods: we included patients admitted to the ICU with the diagnostic of community-acquired pneumonia. Measurements of regional oxygen saturation index (rSO2) were taken using near-infrared spectroscopy technology. The association between this variable and other classical hemodynamic variables and their predictive value for mortality were determined. Results: presence of low rSO2 value was associated with greater mortality. This variables showed better predictive power for mortality than the ones obtained with a vascular occlusion test (AUROC 0.790, IC 95% 0.637-0.943, p=0.004). The presence of low rSO2 at admission and 24 hours after were the only variables that were independently associated with mortality (HR 8.99, IC 95% 1.05-76.8, p=0,045 i HR 13.18, IC 95% 1.52-113.6, p=0.019, respectively). Conclusions: determination of rSO2 can identify which patients with respiratory sepsis present greater severity earlier than other hemodynamical variables

Structure and function of the endothelial glycocalyx in the microcirculation

The endothelial glycocalyx is a thin layer consisting of sugar moieties on the endothelium of the whole vasculature. This layer has been shown to play a role in inflammation coagulation and permeability in the vasculature. In this thesis we studied the structure and composition of the endothelial glycocalyx. We developed a model to induce an anti-inflammatory endothelial glycocalyx in vitro, using physiolgoical shear stress. Furthermore, we studied the role of this glycocalyx in the glomerular capillaries. Here we show that the endothelial glycocalyx contributes to the filtration barrier in the glomeruli. Consequently this implies that damage of this glycocalyx might be a first step in the development of vasculature-born renal failure, like in Type 2 diabetes. The other way around, we also studied the effect of renal failure on the systemic glycocalyx. Using a non-invasive method, we estimated glycocalyx thickness in the sublingual vasculature of patients with end stage renal disease and patients who received a kidney transplant. Interestingly, the endothelial glycocalyx was highly perturbed during end stage renal disease, but comparable to healthy controls after a kindye transplantation. Altogether the endothelial glycocalyx might be a central mediator in the development of both renal and cardiovascular disease.UBL - phd migration 201

Mikroverenkierto ja hemoreologia kriittisesti sairailla potilailla

The study was a prospective observational and methodological study performed among thirty-six critically-ill patients and twenty-six healthy controls subjects in 2008-2012 in two Finnish intensive care units. In critically-ill patients the blood flow among the microcirculation becomes disturbed, which predisposes the patients to multiple organ failure and death. The endothelial glycocalyx layer, which is formed on the vascular surface of endothelial cells is implicated in microcirculatory events in animal studies, but the data among critically-ill patients is scarce and based on laboratory samples only. The viscosity of plasma determines shearing forces of blood, and thus, the shear induced excretion of nitric oxide by the endothelial cells, i.e. mechanosensing. In animal models, increased plasma viscosity is associated with increased microvascular flow. Futhermore, the technology of microvascular and glycocalyx research in humans is under development. The evidence of molecular mechanisms and causal relation between endothelial glycocalyx damage and microcvascular disturbance in critically-ill patients is lacking. The feasibility and reliability of a standardized technical quality analysis for video images obtained from human sublingual microcirculation was tested in the first part of the study. By analysis of a novel previously unvalidated set of technical criteria by two independent investigators, only 31% of the analyzed 240 video images qualified techically for further use in clinical studies. In the second part of the study, a semi-automatic computer algorithm was created and validated for the measurement of glycocalyx layer thickness. Use of the semi-automatic algorithm in microcirculatory video images obtained from human oral cavity diminished the coefficient of variation of measured glycocalyx layer thickness from 7.2% - 9.8% in manual measurements to 4.3% - 5.8% in the semi-automatic measurements. Two separate hypothesis were tested in the third and fourth parts of the study. A hypothesis that activation of vascular adhesion protein-1, a novel adhesion epitope and enzyme, coincides with shedding of the glycocalyx in sepsis, was supported. The second hypothesis, that the shedding of the endothelial glycocalyx layer in sepsis leads to increased plasma viscosity, was rejected. Contrary to the study hypothesis the viscosity of plasma in patients with sepsis was not increased, but was lower than controls values for four days. Ex vivo it was evident that the type of fluid therapy administered during the course of early treatment among critically-ill patients determines plasma viscosity and, thus, the shearing properies of blood in the microcirculation.Väitöskirjatyössä tutkittiin tehohoitoa vaativien potilaiden mikroverenkiertoa ja verenvirtausominaisuuksia. Menetelmiä tarkastelevassa osiossa tarkasteltiin elimistön pienimpien verisuonten tutkimuksessa käytettävän videomikroskopiamenetelmän virhelähteitä sekä kehitettiin uusi tietokonepohjaiseen kuvankäsittelyyn perustuva mittausalgoritmi verisuonen sisäkettokerroksen soluja verhoavan pinnan sokeripitoisista molekyyleistä koostuvan hunnun (t.s. endoteelin glykokalyksin) mittaukseen videokuvasta. Tutkimuksen kliinisen osion kysymyksenasetteluna oli havainnoida esiintyykö kahdellakymmenellä bakteerien aiheuttamaa verenmyrkytystä sairastavalla potilaalla kohonneita endoteelin glykokalyksin vaurion merkkiaineita syndekaani-1:tä (SDC-1) ja hyaluronaania (HA) samanaikaisesti yleistyneen tulehdusreaktion merkkiaineiden myeloperoksidaasin (MPO) ja vascular adhesion protein-1 (VAP-1) kanssa 24 tunnin kuluessa tehohoitoon saapumisesta sekä kolme vuorokautta myöhemmin, verrattaessa kahteenkymmeneen terveeseen verrokkiin. Toisena kysymyksenasetteluna samoilta tutkimushenkilöiltä otetuista verinäytteistä määritettiin suurikokoisten molekyylien pitoisuuksia veren sitkaisuutta, t.s. viskositeettia. Erillisessä elimistön ulkopuolisessa laboratoriotyössä mallinnettiin lisäksi vereen lisättyjen keittosuolan ja suurikokoisten molekyylien (hydroksietyylitärkkelys ja hyaluronaani) sekä samanaikaisesti tapahtuvan veren luonnollisten proteiinien laimenemisen vaikutusta veren sitkaisuuteen. Väitöskirjatyössä tutkittiin tehohoitoa vaativien potilaiden mikroverenkiertoa ja verenvirtausominaisuuksia. Menetelmiä tarkastelevassa osiossa tarkasteltiin elimistön pienimpien verisuonten tutkimuksessa käytettävän videomikroskopiamenetelmän virhelähteitä sekä kehitettiin uusi tietokonepohjaiseen kuvankäsittelyyn perustuva mittausalgoritmi verisuonen sisäkettokerroksen soluja verhoavan pinnan sokeripitoisista molekyyleistä koostuvan hunnun (t.s. endoteelin glykokalyksin) mittaukseen videokuvasta. Tutkimuksen kliinisen osion kysymyksenasetteluna oli havainnoida esiintyykö kahdellakymmenellä bakteerien aiheuttamaa verenmyrkytystä sairastavalla potilaalla kohonneita endoteelin glykokalyksin vaurion merkkiaineita (syndekaani-1:tä ja hyaluronaania) samanaikaisesti yleistyneen tulehdusreaktion merkkiaineiden ( myeloperoksidaasin ja vascular adhesion protein-1:n) kanssa 24 tunnin kuluessa tehohoitoon saapumisesta sekä kolme vuorokautta myöhemmin, verrattaessa kahteenkymmeneen terveeseen verrokkiin. Toisena kysymyksenasetteluna samoilta tutkimushenkilöiltä otetuista verinäytteistä määritettiin suurikokoisten molekyylien pitoisuuksia veren sitkaisuutta, t.s. viskositeettia. Erillisessä elimistön ulkopuolisessa laboratoriotyössä mallinnettiin lisäksi vereen lisättyjen keittosuolan ja suurikokoisten molekyylien (hydroksietyylitärkkelys ja hyaluronaani) sekä samanaikaisesti tapahtuvan veren luonnollisten proteiinien laimenemisen vaikutusta veren sitkaisuuteen. Verrokeilta ja tehohoitoa vaativilta potilailta kerättiin 240 videoleikettä. Videomikroskooppimenetelmän virhelähteiden tunnistamisen perusteella systemaattinen kuvan laadun analysointi ja tieteellinen raportointi on mahdollista. Tutkitussa 240 videoleikkeen aineistossa korkealaatuisen videomateriaalin osuus oli ainoastaan 31%. Tutkimuksessa kehitetyn puoliautomaattisen mittausalgoritmin käyttö pienensi mitatun endoteelin glykokalyksikerroksen paksuuden vaihteluvakiota (4.3% - 5.8%) verrattuna tutkijan käsin, mutta tietokoneavusteisesti, suorittamaan mittaamiseen (7.2% - 9.8%). Kliinisessä osiossa bakteerien aiheuttamaa verenmyrkytystä sairastavilta potilailta mitattiin samanaikaisesti merkittävästi kohonneita endoteelin glykokalyksikerroksen vaurion ja yleistyneen tulehdusreaktion merkkinaineita. Veren suurikokoisten proteiinimolekyyylien pitoisuudet ja veren sitkaisuus oli merkittävästi vähäisempiä kuin verrokeilla. Elimistön ulkopuolisen mallintamisen perusteella potilaille tehohoidossa annettu nestehoito vaikuttaa suuresti veren sitkaisuuteen ja kliinisessä tutkimusosiossa havaittuihin veren sitkaisuuden mittausarvoihin