Hyperspectral Digital Holography for Bio-tissue Segmentation

Hyperspectral digital holography is a relatively new imaging method. This work discusses and demonstrates its advantages compared to traditional imaging methods. The main problem with current imaging systems is that they do not capture transparent objects or their shapes very well. This is especially important in cells and tissues, which consist mostly of water and are thus transparent. Holography has the advantage of utilizing the full complex amplitude, instead of just its intensity. It can be utilized in different detection and segmentation problems, but here the focus is in biotechnology and tissue segmentation. The hyperspectral imaging process in this work consists of capturing diffracted images of the sample at different wavelengths, backpropagating the diffracted images to correct focus and then segmenting the acquired image stack. A lensless capturing setup is used, which has the advantage of having no chromatic aberration. The imaging process in an adaptation of the Fourier transform spectrometer, which requires only one scan to get the full hyperspectral holographic information. The phase delay for the spectrometer is created by adjusting the optical distance of one of the wavefronts in the system. This is done by a mirror controlled by a piezotransducer. To be able to capture hyperspectral information, a supercontinuum laser source is used. The backpropagation is performed with the angular spectrum method, which is computationally efficient. Segmentation is done using k-means clustering in MATLAB. The results show that hyperspectral digital holography is better for capturing transparent objects due to the phase information and wide wavelength spectra. Some of the possible error sources and complications in the process are also discussed. Chapter 1 looks at some of the most recent studies regarding the subject. Chapter 2 describes the theory of wave optics and Fourier transforms necessary for this work. Chapter 3 illustrates the practical process for capturing, reconstructing and segmenting the images. In chapter 4 the resulting segmented images are discussed and chapter 5 concludes the wor

Hyperspectral Digital Holography for Bio-tissue Segmentation

Hyperspectral digital holography is a relatively new imaging method. This work discusses and demonstrates its advantages compared to traditional imaging methods. The main problem with current imaging systems is that they do not capture transparent objects or their shapes very well. This is especially important in cells and tissues, which consist mostly of water and are thus transparent. Holography has the advantage of utilizing the full complex amplitude, instead of just its intensity. It can be utilized in different detection and segmentation problems, but here the focus is in biotechnology and tissue segmentation. The hyperspectral imaging process in this work consists of capturing diffracted images of the sample at different wavelengths, backpropagating the diffracted images to correct focus and then segmenting the acquired image stack. A lensless capturing setup is used, which has the advantage of having no chromatic aberration. The imaging process in an adaptation of the Fourier transform spectrometer, which requires only one scan to get the full hyperspectral holographic information. The phase delay for the spectrometer is created by adjusting the optical distance of one of the wavefronts in the system. This is done by a mirror controlled by a piezotransducer. To be able to capture hyperspectral information, a supercontinuum laser source is used. The backpropagation is performed with the angular spectrum method, which is computationally efficient. Segmentation is done using k-means clustering in MATLAB. The results show that hyperspectral digital holography is better for capturing transparent objects due to the phase information and wide wavelength spectra. Some of the possible error sources and complications in the process are also discussed. Chapter 1 looks at some of the most recent studies regarding the subject. Chapter 2 describes the theory of wave optics and Fourier transforms necessary for this work. Chapter 3 illustrates the practical process for capturing, reconstructing and segmenting the images. In chapter 4 the resulting segmented images are discussed and chapter 5 concludes the wor

Deep convolutional neural network-based lensless quantitative phase retrieval

In this paper, we employ a deep convolutional neural network for the solution of the phase retrieval problem in a lensless optical system from a single observation. We utilize U-net-like structured DCNN to reconstruct phase from the amplitude images at the sensor plane, and after applying computational backpropagation, the complex objects’ amplitude is reconstructed at the object plane. Results are demonstrated by simulation experiments.publishedVersionPeer reviewe

Tannins of Conifer Bark as Nordic Piquancy-Sustainable Preservative and Aroma?

Bark of Norway spruce and Scots pine trees contain large amounts of condensed tannins. Tannins extracted with hot water could be used in different applications as they possess antioxidative and antimicrobial activities. The use of bark tannins as e.g., food preservatives calls for increases in our knowledge of their antioxidative activities when applied in foodstuffs. To assess the ability of bark tannins to prevent lipid oxidation, hot water extracts were evaluated in a liposome model. Isolated tannins were also applied in dry-cured, salty meat snacks either as liquid extracts or in dry-powder form. Consumer acceptance of the snacks was tested by a sensory evaluation panel where outlook, odor, taste, and structure of the snacks were evaluated and compared to a commercial product without tannin ingredients. Our results show that conifer bark tannin-rich extracts have high capacity to prevent lipid oxidation in the liposome model. The efficacies of pine and spruce bark extracts were ten to hundred folds higher, respectively, than those of phenolic berry extracts. The bark extracts did not significantly influence the odor or taste of the meat snacks. The findings indicate that bark extracts may be used as sustainable food ingredients. However, more research is needed to verify their safety.Peer reviewe

Chemical composition and bioactivity of hemp, reed canary grass and common reed grown on boreal marginal lands

Underutilised agricultural land and former peat production areas in northern Europe are potentially suitable for growing lignocellulosic biomass that could be used in various non-food applications. In this study, the biorefining process of Phalaris arundinacea (reed canary grass), Phragmites australis (common reed), and Cannabis sativa (oil and fibre hemp cultivars) was assessed based on their chemical composition and biological activity using various analytical techniques. Two-stage accelerated solvent extraction was used first with hexane, followed by EtOH/H2O (95/5, v/v) to extract the lipophilic and hydrophilic fractions of the samples collected during and after the growing season. Later, pressurised hot water extraction (PHWE) and two-stage extraction were performed to examine the biorefinery potential of aqueous extracts focusing on extraction efficiency, quality, and chemical composition of the plant materials. Combining two-stage and elevated extraction temperatures with PHWE resulted in high levels of total dissolved solids (TDS), carbohydrates, phenolics, and bioactivities. Data showed that TDS yielded over 400 mg g−1 for summer oil hemp and approximately 300 mg g−1 for reed canary grass and common reed. Summer-harvested plants had carbohydrate yields of 110–155 mg g−1, while autumn yields were 40–60 mg g−1 for hemp and 120–170 mg g−1 for reed canary grass and common reed, respectively. The findings suggest that aboveground biomass from marginal lands holds potential as a valuable source of bioactive compounds for biorefinery feedstocks, thereby presenting new opportunities for sustainable biomass-based valorisation and future optimisation of two-stage extraction methods targeting hemicellulose-rich fractions

Inspired by nature: Fiber networks functionalized with tannic acid and condensed tannin-rich extracts of Norway spruce bark show antimicrobial efficacy

This study demonstrated the antibacterial and antiviral potential of condensed tannins and tannic acid when incorporated into fiber networks tested for functional material purposes. Condensed tannins were extracted from industrial bark of Norway spruce by using pressurized hot water extraction (PHWE), followed by purification of extracts by using XADHP7 treatment to obtain sugar-free extract. The chemical composition of the extracts was analyzed by using HPLC, GC‒MS and UHPLC after thiolytic degradation. The test matrices, i.e., lignocellulosic handsheets, were produced and impregnated with tannin-rich extracts, and tannic acid was used as a commercial reference. The antibacterial and antiviral efficacy of the handsheets were analyzed by using bioluminescent bacterial strains (Staphylococcus aureus RN4220+pAT19 and Escherichia coli K12+pCGLS11) and Enterovirus coxsackievirus B3. Potential bonding of the tannin-rich extract and tannic acid within the fiber matrices was studied by using FTIR-ATR spectroscopy. The deposition characteristics (distribution and accumulation patterns) of tannin compounds and extracts within fiber networks were measured and visualized by direct chemical mapping using time-of-flight secondary ion mass spectrometry (ToF-SIMS) and digital microscopy. Our results demonstrated for the first time, how tannin-rich extracts obtained from spruce bark side streams with green chemistry possess antiviral and antibacterial properties when immobilized into fiber matrices to create substitutes for plastic hygienic products, personal protection materials such as surgical face masks, or food packaging materials to prolong the shelf life of foodstuffs and prevent the spread of infections. However, more research is needed to further develop this proof-of-concept to ensure stable chemical bonding in product prototypes with specific chemistry

Toxicological and bioactivity evaluation of blackcurrant press cake, sea buckthorn leaves and bark from Scots pine and Norway spruce extracts under a green integrated approach

Aqueous extracts from blackcurrant press cake (BC), Norway spruce bark (NS), Scots pine bark (SP), and sea buckthorn leaves (SB) were obtained using maceration and pressurized hot water and tested for their bioactivities. Maceration provided the extraction of higher dry matter contents, including total phenolics (TPC), anthocyanins, and condensed tannins, which also impacted higher antioxidant activity. NS and SB extracts presented the highest mean values of TPC and antioxidant activity. Individually, NS extract presented high contents of proanthocyanidins, resveratrol, and some phenolic acids. In contrast, SB contained a high concentration of ellagitannins, ellagic acid, and quercetin, explaining the antioxidant activity and antibacterial effects. SP and BC extracts had the lowest TPC and antioxidant activity. However, BC had strong antiviral efficacy, whereas SP can be considered a potential ingredient to inhibit α-amylase. Except for BC, the other extracts decreased reactive oxygen species (ROS) generation in HCT8 and A549 cells. Extracts did not inhibit the production of TNF-alpha in lipopolysaccharide-stimulated THP-1 macrophages but inhibited the ROS generation during the THP-1 cell respiratory burst. The recovery of antioxidant compounds from these by-products is incentivized for high value-added applications.</p

Remdesiviiri sairaalahoitoisessa COVID-19-taudissa : pragmaattinen, adaptiivinen, satunnaistettu Solidarity Finland -monikeskustutkimus

Lähtökohdat : Remdesiviiriä tutkittiin Solidarity Finland -tutkimuksessa. Menetelmät : COVID-19-taudin takia sairaalahoitoon joutuneet potilaat satunnaistettiin saamaan standardihoitoa tai sen lisäksi remdesiviiriä. Solidarity-tutkimuksessa ja satunnaistettujen ­tutkimusten meta-analyysissä ensisijainen päätetapahtuma oli sairaalahoitoajan kuolleisuus. Tulokset : Rekrytoimme 208 potilasta yhdestätoista sairaalasta. Sairaalahoidon aikana ­remdesiviiriryhmässä (n = 114) kuoli 1 % ja standardihoitoryhmässä (n = 94) 4 %. Invasiiviseen hengityslaitehoitoon joutui 5 % molemmissa ryhmissä. Tehohoitoa sai 11 % remdesiviiri- ja 12 % standardihoitoryhmässä. Maksaentsyymit nousivat merkittävästi 5 %:lla remdesiviiri- ja 2 %:lla standardihoitoryhmässä. Meta-analyysin alaryhmäanalyysissä remdesiviiri vähensi kuoleman riskiä potilailla, jotka eivät sairaalahoidon alkaessa saaneet hengityslaitehoitoa (RR 0,85, 95 % LV 0,75­–0,96). Päätelmät : Suomessa on pandemian aikana mahdollista rekrytoida merkittävä määrä potilaita suuriin, satunnaistettuihin tutkimuksiin, joilla voidaan saada luotettavia tuloksia nopeasti. Remdesiviiristä voi olla apua sairaalahoitoisessa COVID-19-taudissa varhain aloitettuna.publishedVersionPeer reviewe

Effect of remdesivir post hospitalization for COVID-19 infection from the randomized SOLIDARITY Finland trial

We report the first long-term follow-up of a randomized trial (NCT04978259) addressing the effects of remdesivir on recovery (primary outcome) and other patient-important outcomes one year after hospitalization resulting from COVID-19. Of the 208 patients recruited from 11 Finnish hospitals, 198 survived, of whom 181 (92%) completed follow-up. At one year, self-reported recovery occurred in 85% in remdesivir and 86% in standard of care (SoC) (RR 0.94, 95% CI 0.47-1.90). We infer no convincing difference between remdesivir and SoC in quality of life or symptom outcomes (p > 0.05). Of the 21 potential long-COVID symptoms, patients reported moderate/major bother from fatigue (26%), joint pain (22%), and problems with memory (19%) and attention/concentration (18%). In conclusion, after a one-year follow-up of hospitalized patients, one in six reported they had not recovered well from COVID-19. Our results provide no convincing evidence of remdesivir benefit, but wide confidence intervals included possible benefit and harm.Peer reviewe

Tiedotteen vaikutus yrityksen pörssikurssiin ja uutisointi

Tämä työ lähtee liikkeelle kahdesta alkuolettamasta. Ensinnäkin, osakemarkkinat toimivat tehokkaasti ja siellä vallitsee täydellinen kilpailu. Toisekseen, journalismin taso suomalaisessa mediassa on hyvä ja yritysten tiedotteet analysoidaan ja raportoidaan hyvin ja asiantuntevasti. Työn tavoite on tutkia, toteutuvatko nämä kaksi eri alkuolettamaa. Käytännön syistä tähän työhön valikoitui Helsingin pörssistä viisi yritystä: Nordea, Amer Sports, Stockmann, Nokia ja Elisa. Kaikki ovat suuria yrityksiä, edustavat eri toimialoja ja osakkeet ovat likvidejä. Ajallisesti tiedotteet tutkittiin 1.1.2015 – toisen vuosineljänneksen osavuosikatsaukseen, eli noin kuuden kuukauden ajalta. Työn teoriaan jakautuu pääasiassa kahteen eri osaan. Tässä työssä osaketta tarkastellaan ihan kuin mitä tahansa hyödykettä, eli sillä on omanlaisensa kysyntä ja tarjonta. Teorian mukaan markkina on tasapainossa, kun kysyntä ja tarjonta kohtaavat. Toisaalta, tässä työssä tarkastellaan myös pörssiyhtiön lakisääteistä velvollisuutta raportoida omasta tilanteestaan säännöllisesti ja jatkuvasti. Työ toteutettiin lukemalla yritysten tiedotteita ja antamalla niille joku arvo: positiivinen, neutraali tai negatiivinen. Tiedotteista arvioitiin tällä tavalla sekä sanallinen sävy että varsinaiset tulostiedot. Näitä sitten verrattiin kurssitietoihin. Myös tiedotteen sävy verrattiin siitä kirjoitettuihin juttuihin. Työssä on pienehkö tilastollinen osuus, missä verrataan kurssimuutoksen suuntaa sekä toimialaindeksiin että OMX25-­indeksiin. Tiedotteita ja juttuja arvioitiin tekstianalyysin keinoin. Työ toteutettiin kahdessa vaiheessa lukuvuoden 2015-­2016 aikana. Yritysten tiedotteet ja kurssitiedot on hankittu syksyllä 2015. Näitä tiedotteita vastaavat lehtijutut luettiin Taloussanomien, Kauppalehden, Ylen ja MTV:n sivuilta keväällä 2016. Tiedotteen vaikutusta kurssiin tutkittiin vertaamalla tiedotteen julkaisua edeltävän päivän kurssia julkaisupäivän kurssiin ja kurssiin julkaisupäivää viikon päästä. Työn johtopäätös on, että tulokset vahvistavat alkuolettamukset. Vaikka Helsingin pörssi onkin suhteellisen pieni markkinapaikka, niin kaikki tehokkaan markkinan edellytykset täyttyvät ja markkinoilla on täydellinen kilpailu ostajien ja myyjien kesken. Myös journalismin taso on hyvä, ainakin tässä työssä tarkastelluissa suurimmissa medioissa. Median keskittymisen johdosta, nämä mediat tavoittavat päivittäin suurimman osan suomalaisista