Studies on binaural and monaural signal analysis methods and applications

Sound signals can contain a lot of information about the environment and the sound sources present in it. This thesis presents novel contributions to the analysis of binaural and monaural sound signals. Some new applications are introduced in this work, but the emphasis is on analysis methods. The three main topics of the thesis are computational estimation of sound source distance, analysis of binaural room impulse responses, and applications intended for augmented reality audio. A novel method for binaural sound source distance estimation is proposed. The method is based on learning the coherence between the sounds entering the left and right ears. Comparisons to an earlier approach are also made. It is shown that these kinds of learning methods can correctly recognize the distance of a speech sound source in most cases. Methods for analyzing binaural room impulse responses are investigated. These methods are able to locate the early reflections in time and also to estimate their directions of arrival. This challenging problem could not be tackled completely, but this part of the work is an important step towards accurate estimation of the individual early reflections from a binaural room impulse response. As the third part of the thesis, applications of sound signal analysis are studied. The most notable contributions are a novel eyes-free user interface controlled by finger snaps, and an investigation on the importance of features in audio surveillance. The results of this thesis are steps towards building machines that can obtain information on the surrounding environment based on sound. In particular, the research into sound source distance estimation functions as important basic research in this area. The applications presented could be valuable in future telecommunications scenarios, such as augmented reality audio

Estimation of reverberation time from binaural signals without using controlled excitation

Tässä työssä tutkittiin jälkikaiunta-ajan estimointia binauraalisesta äänisignaalista. Jälkikaiunta-aika (RT) on yksi tärkeimmistä akustisista parametreista, jonka tuntemisesta olisi hyötyä useissa sovelluksissa, kuten laajennetussa äänitodellisuudessa, matkaviestinnässä ja älykkäissä kuulolaitteissa. Tämän tyyppisissä sovelluksissa estimaattia jälkikaiunta-ajasta ei yleensä ole saatavilla eikä sitä ole mahdollista mitata standardimenetelmillä. Jälkikaiunta-ajan estimointia varten kehitettiin automaattinen menetelmä, joka ei vaadi mitään etukäteistietoa ympäröivästä akustisesta tilasta ja toimii mielivaltaisella binauraalisella signaalilla, toisin kuin perinteiset mittausmenetelmät. Algoritmin perusideana on ensin paikantaa jälkikaiunta-analysiin sopivat signaalin osat ja sen jälkeen laskea jälkikaiunta perustuen Schröderin käänteiseen integrointimenetelmään. Jälkikaiunta-aikaestimaatti saadaan lopulta tilastollisen analyysin tuloksena. Binauraalisuutta hyödynnetään käyttämällä kanavien välistä koherenssifunktiota analyysissä. Käänteiseen integrointiin ja sitä seuraavaan suoran sovitukseen liittyvien rajojen etsintään keksittiin muutamia uusia metodeja. Algoritmista totetuttiin reaaliaikaversio C++ -kielellä ja algoritmin toimintaa arvioitiin sekä synteettisillä että todellisilla nauhoitetuilla signaaleilla. Tulokset osoittavat, että algoritmi kykenee estimoimaan jälkikaiunta-ajan melko tarkasti useimmissa tapauksissa, vaikka eri akustisten tilojen välillä onkin vaihtelua.This thesis concentrates on the task of estimating reverberation time from binaural audio signals. The reverberation time (RT) is one of the most important acoustic parameters describing the acoustic behavior of a space. An estimate of this parameter would be advantageous to many audio applications, such as augmented reality audio, mobile communications and intelligent hearing aids. Usually in these kind of applications no estimates of the room acoustic parameters are available and it is not possible to acquire the parameters online using standard measurement techniques. An automatic algorithm for estimating the reverberation time was developed. This algorithm requires no a priori knowledge of the surrounding space and operates on an arbitrary binaural input signal, as opposed to standard acoustic measurement techniques. The basic idea of the algorithm is to first locate suitable signal segments for subsequent analysis and then calculate the reverberation time by applying the standard Schroeder integration method to each segment followed by some statistical analysis to derive a final RT estimate. The binaural nature of the input signals is also taken advantage of by using the inter-channel coherence in the analysis. Some new ideas for finding the integration and line fitting limits were also developed. A real-time version of the algorithm was implemented in C++. The algorithm performance was evaluated with both synthetic signals and real recordings. The results show that the algorithm can determine the reverberation quite accurately in most cases, even though there is some degree of variability between different rooms

Trapping of 27 bp - 8 kbp DNA and immobilization of thiol-modified DNA using dielectrophoresis

Dielectrophoretic trapping of six different DNA fragments, sizes varying from the 27 to 8416 bp, has been studied using confocal microscopy. The effect of the DNA length and the size of the constriction between nanoscale fingertip electrodes on the trapping efficiency have been investigated. Using finite element method simulations in conjunction with the analysis of the experimental data, the polarizabilities of the different size DNA fragments have been calculated for different frequencies. Also the immobilization of trapped hexanethiol- and DTPA-modified 140 nm long DNA to the end of gold nanoelectrodes was experimentally quantified and the observations were supported by density functional theory calculations.Comment: 17 pages (1 column version), 8 figure

UriSed 3 PRO automated microscope in screening bacteriuria at region-wide laboratory organization

Background and aims: We assessed the possibility to rule out negative urine cultures by counting with UriSed 3 PRO (77 Elektmnika, Hungary) at Helsinki and Uusimaa Hospital District. Materials and methods: Bacteria counting of the UriSed 3 PRO automated microscope was verified with reference phase contrast microscopy against growth in culture. After acceptance into routine, results of bacteria and leukocyte counting from 56 426 specimens with eight UriSed 3 PRO instruments were compared against results from parallel samples cultured on chromogenic agar. Laboratory data including preanalytical details were accessed through the regional database of the Helsinki and Uusimaa Hospital District. Results: A combined sensitivity of 87-92% and a negative predictive value of 90-96% with a specificity of 54-50% was reached, depending on criteria. Preanalytical data (incubation time in bladder) combined with the way of urine collection would improve these figures if reliable. Conclusions: Complex patient populations, regional logistics and data interfases, and economics related to increased costs of additional particle counts against costs of screening cultures of all samples, did not support adaptation of a screening process of urine cultures. This conclusion was made locally, and may not be valid elsewhere.Peer reviewe

Identification of proprotein convertase substrates using genome-wide expression correlation analysis

Identification of proprotein convertase substrates using genome-wide expression correlation analysis Turpeinen, Hannu Kukkurainen, Sampo Pulkkinen, Kati Kauppila, Timo Ojala, Kalle Hytonen, Vesa P Pesu, Marko England BMC genomics BMC Genomics. 2011 Dec 20;12:618. engABSTRACT: BACKGROUND: Subtilisin/kexin-like proprotein convertase (PCSK) enzymes have important regulatory function in a wide variety of biological processes. PCSKs proteolytically process at a target sequence that contains basic amino acids arginine and lysine, which results in functional maturation of the target protein. In vitro assays have showed significant biochemical redundancy between the seven family members, but the phenotypes of PCSK deficient mice and patients carrying an inactive PCSK allele argue for a specific biological function. Modeling the structures of individual PCSK enzymes has offered little insights into the specificity determinants. However, previous studies have shown that there can be a coordinated expression between a PCSK and its target molecule. Here, we have surveyed the putative PCSK target proteins using genome-wide expression correlation analysis and cleavage site prediction algorithms. RESULTS: We first performed a gene expression correlation analysis over the whole genome for all PCSK enzymes. PCSKs were found to cluster differently based on the strength of correlations. The screen for putative PCSK target proteins showed a significant enrichment (p-values from 1.2e-4 to <1.0e-10) of putative targets among the most positively correlating genes for most PCSKs. Interestingly, there was no enrichment in putative targets among the genes that correlated positively with the biologically redundant PCSK7, whereas PCSK5 showed an inverse correlation. PCSKs also showed a highly variable degree of shared target genes that were identified by expression correlation and cleavage site prediction. Multiple alignments were used to evaluate the putative targets to pinpoint the important residues for the substrate recognition. Finally, we validated our approach and identified biochemically PAPPA1 and ADAMTS6 as novel targets for FURIN proteolytic activity. CONCLUSIONS: Most PCSK enzymes display strong positive expression correlation with predicted target proteins in our genome-wide analysis. We also show that expression correlation screen combined with a cleavage site-prediction analysis can be used to identify novel bona fide target molecules for PCSKs. Exploring the positively correlating genes can thus offer additional insights into the biology of proprotein convertases.Peer reviewe

The F1 loop of the talin head domain acts as a gatekeeper in integrin activation and clustering

Integrin activation and clustering by talin are early steps of cell adhesion. Membrane-bound talin head domain and kindlin bind to the beta integrin cytoplasmic tail, cooperating to activate the heterodimeric integrin, and the talin head domain induces integrin clustering in the presence of Mn2+. Here we show that kindlin-1 can replace Mn2+ to mediate beta 3 integrin clustering induced by the talin head, but not that induced by the F2-F3 fragment of talin. Integrin clustering mediated by kindlin-1 and the talin head was lost upon deletion of the flexible loop within the talin head F1 subdomain. Further mutagenesis identified hydrophobic and acidic motifs in the F1 loop responsible for beta 3 integrin clustering. Modeling, computational and cysteine crosslinking studies showed direct and catalytic interactions of the acidic F1 loop motif with the juxtamembrane domains of alpha- and beta 3-integrins, in order to activate the beta 3 integrin heterodimer, further detailing the mechanism by which the talin-kindlin complex activates and clusters integrins. Moreover, the F1 loop interaction with the beta 3 integrin tail required the newly identified compact FERM fold of the talin head, which positions the F1 loop next to the inner membrane clasp of the talin-bound integrin heterodimer. This article has an associated First Person interview with the first author of the paper.Peer reviewe

Zebavidin - An avidin-like protein from zebrafish

The avidin protein family members are well known for their high affinity towards D-biotin and high structural stability. These properties make avidins valuable tools for a wide range of biotechnology applications. We have identified a new member of the avidin family in the zebrafish (Danio rerio) genome, hereafter called zebavidin. The protein is highly expressed in the gonads of both male and female zebrafish and in the gills of male fish, but our data suggest that zebavidin is not crucial for the developing embryo. Biophysical and structural characterisation of zebavidin revealed distinct properties not found in any previously characterised avidins. Gel filtration chromatography and native mass spectrometry suggest that the protein forms dimers in the absence of biotin at low ionic strength, but assembles into tetramers upon binding biotin. Ligand binding was analysed using radioactive and fluorescently labelled biotin and isothermal titration calorimetry. Moreover, the crystal structure of zebavidin in complex with biotin was solved at 2.4 Å resolution and unveiled unique ligand binding and subunit interface architectures; the atomic-level details support our physicochemical observations.Public Library of Science open acces

Construction of Chimeric Dual-Chain Avidin by Tandem Fusion of the Related Avidins

BACKGROUND: Avidin is a chicken egg-white protein with high affinity to vitamin H, also known as D-biotin. Many applications in life science research are based on this strong interaction. Avidin is a homotetrameric protein, which promotes its modification to symmetrical entities. Dual-chain avidin, a genetically engineered avidin form, has two circularly permuted chicken avidin monomers that are tandem-fused into one polypeptide chain. This form of avidin enables independent modification of the two domains, including the two biotin-binding pockets; however, decreased yields in protein production, compared to wt avidin, and complicated genetic manipulation of two highly similar DNA sequences in the tandem gene have limited the use of dual-chain avidin in biotechnological applications. PRINCIPAL FINDINGS: To overcome challenges associated with the original dual-chain avidin, we developed chimeric dual-chain avidin, which is a tandem fusion of avidin and avidin-related protein 4 (AVR4), another member of the chicken avidin gene family. We observed an increase in protein production and better thermal stability, compared with the original dual-chain avidin. Additionally, PCR amplification of the hybrid gene was more efficient, thus enabling more convenient and straightforward modification of the dual-chain avidin. When studied closer, the generated chimeric dual-chain avidin showed biphasic biotin dissociation. SIGNIFICANCE: The improved dual-chain avidin introduced here increases its potential for future applications. This molecule offers a valuable base for developing bi-functional avidin tools for bioseparation, carrier proteins, and nanoscale adapters. Additionally, this strategy could be helpful when generating hetero-oligomers from other oligomeric proteins with high structural similarity

Suomen kansantalouden materiaalivirrat ja niiden vaikutukset : Toteutunut kehitys ja kiertotalouden skenaariot vuodelle 2035

Tutkimuksen tavoitteena oli lisätä ymmärrystä kiertotalouden potentiaalista vaikuttaa Suomen luonnonvarojen käyttöön ja niistä aiheutuviin ympäristö- ja talousvaikutuksiin. Viimeaikaisen kehityksen lisäksi arvioitiin kolmea luonnonvarojen käytön skenaariota vuodelle 2035. Niihin lisättiin kiertotaloustoimenpiteitä vaiheittain siten, että kunniahimoisin skenaario pyrki saavuttamaan Suomen kiertotalouden strategisen ohjelman luonnonvaratavoitteiden lisäksi myös Suomen hiilineutraalisuustavoitteen. Tulosten perusteella kiertotalouden strategisessa ohjelmassa asetut luonnonvaratavoitteet ovat osin saavutettavissa. Tällöin Suomen raaka-aineiden kokonaiskulutus vuonna 2035 ei ylitä vuoden 2015 tasoa, ja materiaalien kiertotalousaste kaksinkertaistuu vuodesta 2015. Myös hiilineutraalisuus voidaan saavuttaa vuoteen 2035 mennessä työssä hahmoteltujen oletuksien ja lisätoimien toteutuessa. Puhdas energiasiirtymä vähentää Suomen päästöjä ja luonnonvarojen käyttöä merkittävästi jo nykyisten päätösten toteutuessa perusskenaariossa. Kiertotaloustoimenpiteet edistävät edelleen päästöjen laskua ja vahvistavat nieluja. Suomen raaka-aineiden kulutus asukasta kohden säilyy kiertotaloustoimenpiteistä huolimatta globaalisti erittäin korkealla tasolla ja resurssituottavuudessa jäädään kauas EU-maiden keskiarvosta. Kiertotalouden toteutukseen tarvitaan lisää kunnianhimoa ja toimintaa tukevia ohjauskeinoja. Julkaisu on päivitetty 22.3.2024, s. 21, 23, 43, 89

Significant increase in azithromycin “resistance” and susceptibility to ceftriaxone and cefixime in Neisseria gonorrhoeae isolates in 26 European countries, 2019

Euro-GASP network: Claudia Eder, Sonja Pleininger, Steliana Huhlescu, Irith de Baetselier, Blaženka Hunjak, Tatjana Nemeth Blažić, Panagiota Maikanti-Charalampous, Despo Pieridou, Hana Zákoucká, Helena Žemličková, Steen Hoffmann, Susan Cowan, Rita Peetso, Jelena Viktorova, Ndeindo Ndeikoundam, Beatrice Bercot, Anu Patari Sampo, Vesa Kirjavainen, Susanne Buder, Klaus Jansen, Vivi Miriagou, Eszter Balla, Mária Dudás, Guðrún Sigmundsdóttir, Lena Ros Asmundsdottir, Sinead Saab, Brendan Crowley, Anna Carannante, Paola Stefanelli, Gatis Pakarna, Violeta Mavcutko, Robert Cassar, Christopher Barbara, Francesca Vella, Alje Van Dam, Ineke Linde, Dominique Caugant, Hilde Kløvstad, Beata Mlynarczyk-Bonikowska, Maria-José Borrego, Peter Pavlik, Irena Klavs, Tanja Kustec, Julio Vazquez, Asuncion Diaz, Raquel Abad Torreblanca, Inga Velicko, Magnus Unemo, Helen Fifer, Kate TempletonBackground: The European Gonococcal Antimicrobial Surveillance Programme (Euro-GASP) performs annual sentinel surveillance of Neisseria gonorrhoeae susceptibility to therapeutically relevant antimicrobials across the European Union/European Economic Area (EU/EEA). We present the Euro-GASP results from 2019 (26 countries), linked to patient epidemiological data, and compared with data from previous years. Methods: Agar dilution and minimum inhibitory concentration (MIC) gradient strip methodologies were used to determine the antimicrobial susceptibility (using EUCAST clinical breakpoints, where available) of 3239 N. gonorrhoeae isolates from 26 countries across the EU/EEA. Significance of differences compared with Euro-GASP results in previous years was analysed using Z-test and the Pearson's χ2 test was used to assess significance of odds ratios for associations between patient epidemiological data and antimicrobial resistance. Results: European N. gonorrhoeae isolates collected between 2016 and 2019 displayed shifting MIC distributions for; ceftriaxone, with highly susceptible isolates increasing over time and occasional resistant isolates each year; cefixime, with highly-susceptible isolates becoming increasingly common; azithromycin, with a shift away from lower MICs towards higher MICs above the EUCAST epidemiological cut-off (ECOFF); and ciprofloxacin which is displaying a similar shift in MICs as observed for azithromycin. In 2019, two isolates displayed ceftriaxone resistance, but both isolates had MICs below the azithromycin ECOFF. Cefixime resistance (0.8%) was associated with patient sex, with resistance higher in females compared with male heterosexuals and men-who-have-sex-with-men (MSM). The number of countries reporting isolates with azithromycin MICs above the ECOFF increased from 76.9% (20/26) in 2016 to 92.3% (24/26) in 2019. Isolates with azithromycin MICs above the ECOFF (9.0%) were associated with pharyngeal infection sites. Following multivariable analysis, ciprofloxacin resistance remained associated with isolates from MSM and heterosexual males compared with females, the absence of a concurrent chlamydial infection, pharyngeal infection sites and patients ≥ 25 years of age. Conclusions: Resistance to ceftriaxone and cefixime remained uncommon in EU/EEA countries in 2019 with a significant decrease in cefixime resistance observed between 2016 and 2019. The significant increase in azithromycin "resistance" (azithromycin MICs above the ECOFF) threatens the effectiveness of the dual therapy (ceftriaxone + azithromycin), i.e., for ceftriaxone-resistant cases, currently recommended in many countries internationally and requires close monitoring.The study was funded by the European Centre for Disease Prevention and Control (Framework Contract No. ECDC/2017/004).info:eu-repo/semantics/publishedVersio