Sherali-Adams Relaxations and Indistinguishability in Counting Logics

Two graphs with adjacency matrices $\mathbf{A}$ and $\mathbf{B}$ are isomorphic if there exists a permutation matrix $\mathbf{P}$ for which the identity $\mathbf{P}^{\mathrm{T}} \mathbf{A} \mathbf{P} = \mathbf{B}$ holds. Multiplying through by $\mathbf{P}$ and relaxing the permutation matrix to a doubly stochastic matrix leads to the linear programming relaxation known as fractional isomorphism. We show that the levels of the Sherali--Adams (SA) hierarchy of linear programming relaxations applied to fractional isomorphism interleave in power with the levels of a well-known color-refinement heuristic for graph isomorphism called the Weisfeiler--Lehman algorithm, or, equivalently, with the levels of indistinguishability in a logic with counting quantifiers and a bounded number of variables. This tight connection has quite striking consequences. For example, it follows immediately from a deep result of Grohe in the context of logics with counting quantifiers that a fixed number of levels of SA suffice to determine isomorphism of planar and minor-free graphs. We also offer applications in both finite model theory and polyhedral combinatorics. First, we show that certain properties of graphs, such as that of having a flow circulation of a prescribed value, are definable in the infinitary logic with counting with a bounded number of variables. Second, we exploit a lower bound construction due to Cai, Fürer, and Immerman in the context of counting logics to give simple explicit instances that show that the SA relaxations of the vertex-cover and cut polytopes do not reach their integer hulls for up to $\Omega(n)$ levels, where $n$ is the number of vertices in the graph.

Improving algorithm speed in PNL mixture separation and Wiener system inversion

This paper proposes a very simple method for increasing the algorithm speed for separating sources from PNL mixtures or invertingWiener systems. The method is based on a pertinent initialization of the inverse system, whose computational cost is very low. The nonlinear part is roughly approximated by pushing the observations to be Gaussian; this method provides a surprisingly good approximation even when the basic assumption is not fully satisfied. The linear part is initialized so that outputs are decorrelated. Experiments shows the impressive speed improvement.

The structure of human tRNALys3 anticodon bound to HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs

Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNA(Lys3), to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3'-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5'-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNA(Lys3). The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s(2)U(34), and pseudouridine, Psi(39), appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U(162)*Psi(39) and G(163)*A(38), that maintained a reasonable A-form helix diameter. The tRNA's s(2)U(34) stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Psi(39) stabilized the adjacent mismatched pairs.

New Algorithm for Managing Childhood Illness Using Mobile Technology (ALMANACH): A Controlled Non-Inferiority Study on Clinical Outcome and Antibiotic Use in Tanzania.

INTRODUCTION: The decline of malaria and scale-up of rapid diagnostic tests calls for a revision of IMCI. A new algorithm (ALMANACH) running on mobile technology was developed based on the latest evidence. The objective was to ensure that ALMANACH was safe, while keeping a low rate of antibiotic prescription. METHODS: Consecutive children aged 2-59 months with acute illness were managed using ALMANACH (2 intervention facilities), or standard practice (2 control facilities) in Tanzania. Primary outcomes were proportion of children cured at day 7 and who received antibiotics on day 0. RESULTS: 130/842 (15∙4%) in ALMANACH and 241/623 (38∙7%) in control arm were diagnosed with an infection in need for antibiotic, while 3∙8% and 9∙6% had malaria. 815/838 (97∙3%;96∙1-98.4%) were cured at D7 using ALMANACH versus 573/623 (92∙0%;89∙8-94∙1%) using standard practice (p<0∙001). Of 23 children not cured at D7 using ALMANACH, 44% had skin problems, 30% pneumonia, 26% upper respiratory infection and 13% likely viral infection at D0. Secondary hospitalization occurred for one child using ALMANACH and one who eventually died using standard practice. At D0, antibiotics were prescribed to 15∙4% (12∙9-17∙9%) using ALMANACH versus 84∙3% (81∙4-87∙1%) using standard practice (p<0∙001). 2∙3% (1∙3-3.3) versus 3∙2% (1∙8-4∙6%) received an antibiotic secondarily. CONCLUSION: Management of children using ALMANACH improve clinical outcome and reduce antibiotic prescription by 80%. This was achieved through more accurate diagnoses and hence better identification of children in need of antibiotic treatment or not. The building on mobile technology allows easy access and rapid update of the decision chart. TRIAL REGISTRATION: Pan African Clinical Trials Registry PACTR201011000262218.

Toward on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking: development and benchmark of a scoring function.

We address the challenges of treating polarization and covalent interactions in docking by developing a hybrid quantum mechanical/molecular mechanical (QM/MM) scoring function based on the semiempirical self-consistent charge density functional tight-binding (SCC-DFTB) method and the CHARMM force field. To benchmark this scoring function within the EADock DSS docking algorithm, we created a publicly available dataset of high-quality X-ray structures of zinc metalloproteins ( http://www.molecular-modelling.ch/resources.php ). For zinc-bound ligands (226 complexes), the QM/MM scoring yielded a substantially improved success rate compared to the classical scoring function (77.0% vs 61.5%), while, for allosteric ligands (55 complexes), the success rate remained constant (49.1%). The QM/MM scoring significantly improved the detection of correct zinc-binding geometries and improved the docking success rate by more than 20% for several important drug targets. The performance of both the classical and the QM/MM scoring functions compare favorably to the performance of AutoDock4, AutoDock4Zn, and AutoDock Vina.

Development of phase retrieval algorithm and techniques for optical spectrum analysis

Coherent anti-Stokes Raman scattering is the powerful method of laser spectroscopy in which significant successes are achieved. However, the non-linear nature of CARS complicates the analysis of the received spectra. The objective of this Thesis is to develop a new phase retrieval algorithm for CARS. It utilizes the maximum entropy method and the new wavelet approach for spectroscopic background correction of a phase function. The method was developed to be easily automated and used on a large number of spectra of different substances.. The algorithm was successfully tested on experimental data.

Stellar population synthesis: the effect of improved Asymptotic Giant Branch models and of interstellar dust on mass-to-light–color relations

Teoreettisen populaatiosynteesin avulla voidaan mallintaa tähtijoukkojen ja galaksien fotometrisiä ominaisuuksia yhdistämällä yksittäisten tähtien tuottama säteily, joka saadaan teoreettisista tähtien kehitysmalleista. Valitsemalla sopiva massajakauma syntyville tähdille voidaan muodostaa yksinkertainen tähtipopulaatio, joka koostuu saman ikäisistä ja kemialliselta koostumukseltaan yhtenäisistä tähdistä. Monimutkaisempia tähtipopulaatioita voidaan muodostaa konvoloimalla yksinkertaisten tähtipopulaatioiden luminositeetti jonkin valitun tähtienmuodostushistorian kanssa sekä yhdistämällä näin muodostettuja populaatioita. Tässä työssä tarkastellaan asymptoottisen jättiläishaaran (AGB) tähtien uusien, tarkentuneiden evoluutiomallien vaikutusta populaatiosynteesin tuloksiin niin yksinkertaisten tähtipopulaatioiden kuin galaksien mallinnukseen soveltuvien monimutkaisempien tähtipopulaatioiden kohdalla. Työn päätarkoitus on tuottaa uudistuneisiin malleihin perustuvat populaation massa-luminositeetti -suhteen ja värin väliset relaatiot (MLC-relaatiot). MLC-relaatioita voidaan käyttää populaation massan määrittämiseen sen fotometristen ominaisuuksien (väri, luminositeetti) perusteella. Lisäksi tutkitaan tähtienvälisen pölyn vaikutusta yksinkertaisen spiraaligalaksimallin MLC-relaatioihin. Työssä käytetyt tähtien kehitysmallit perustuvat julkaisuun Marigo et al. (Astronomy & Astrophysics 482, 2008). Havaitaan, että AGB-tähtien vaikutus populaation integroituun luminositeettiin on pieni näkyvillä aallonpituuksilla, mutta merkittävä lähi-infrapuna-alueella. Vaikutus MLC-relaatioihin on vastaavasti merkittävä tarkkailtaessa luminositeettia lähi-infrapunassa sekä käytettäessä värejä, joissa yhdistetään optisia ja lähi-infrapunan kaistoja. Todetaan, että MLC-relaatioiden käyttö lähi-infrapunassa edellyttää tarkentuneen AGB-vaiheen sisällyttämistä populaatiosynteesin malleihin. Tähtienvälisen pölyn vaikutus MLC-relaatioihin todetaan riippuvan käytetystä kaistasta ja väristä, mutta vaikutuksen havaitaan olevan suurin optisen ja lähi-infrapunan väriyhdistelmillä.

Leaf-Targeted Ferredoxin-NADP+-Oxidoreductase (FNR): Electron Transfer Properties and Thylakoid Association in Arabidopsis thaliana

Photosynthetic reactions are divided in two parts: light-driven electron transfer reactions and carbon fixation reactions. Electron transfer reactions capture solar energy and split water molecules to form reducing energy (NADPH) and energy-carrying molecules (ATP). These end-products are used for fixation of inorganic carbon dioxide into organic sugar molecules. Ferredoxin-NADP⁺ oxidoreductase (FNR) is an enzyme that acts at the branch point between the electron transfer reactions and reductive metabolism by catalyzing reduction of NADP+ at the last step of the electron transfer chain. In this thesis, two isoforms of FNR from A rabidopsis thaliana, FNR1 and FNR2, were characterized using the reverse genetics approach. The fnr1 and fnr2 mutant plants resembled each other in many respects. Downregulation of photosynthesis protected the single fnr mutant plants from excess formation of reactive oxygen species (ROS), even without significant upregulation of antioxidative mechanisms. Adverse growth conditions, however, resulted in phenotypic differences between fnr1 and fnr2. While fnr2 plants showed downregulation of photosynthetic complexes and upregulation of antioxidative mechanisms under low-temperature growth conditions, fnr1 plants had the wild-type phenotype, indicating that FNR2 may have a specific role in redistribution of electrons under unfavorable conditions. The heterozygotic double mutant (fnr1xfnr2) was severely devoid of chloroplastic FNR, which clearly restricted photosynthesis. The fnr1xfnr2 plants used several photoprotective mechanisms to avoid oxidative stress. In wild-type chloroplasts, both FNR isoforms were found from the stroma, the thylakoid membrane, and the inner envelope membrane. In the absence of the FNR1 isoform, FNR2 was found only in the stroma, suggesting that FNR1 and FNR2 form a dimer, by which FNR1 anchors FNR2 to the thylakoid membrane. Structural modeling predicted formation of an FNR dimer in complex with ferredoxin. In this thesis work, Tic62 was found to be the main protein that binds FNR to the thylakoid membrane, where Tic62 and FNR formed high molecular weight complexes. The formation of such complexes was shown to be regulated by the redox state of the chloroplast. The accumulation of Tic62-FNR complexes in darkness and dissociation of complexes from the membranes in light provide evidence that the complexes may have roles unrelated to photosynthesis. This and the high viability of fnr1 mutant plants lacking thylakoid-bound FNR indicate that the stromal pool of FNR is photosynthetically active.

Stress testing and risk evaluation of new capacity payment algorithm proposed by Market Council

In the Russian Wholesale Market, electricity and capacity are traded separately. Capacity is a special good, the sale of which obliges suppliers to keep their generating equipment ready to produce the quantity of electricity indicated by the System Operator. The purpose of the formation of capacity trading was the maintenance of reliable and uninterrupted delivery of electricity in the wholesale market. The price of capacity reflects constant investments in construction, modernization and maintenance of power plants. So, the capacity sale creates favorable conditions to attract investments in the energy sector because it guarantees the investor that his investments will be returned.

Solving Leontief Input-Output Model with Trapezoidal Fuzzy Numbers and Gauss-Seidel Algorithm

In this work a fuzzy linear system is used to solve Leontief input-output model with fuzzy entries. For solving this model, we assume that the consumption matrix from di erent sectors of the economy and demand are known. These assumptions heavily depend on the information obtained from the industries. Hence uncertainties are involved in this information. The aim of this work is to model these uncertainties and to address them by fuzzy entries such as fuzzy numbers and LR-type fuzzy numbers (triangular and trapezoidal). Fuzzy linear system has been developed using fuzzy data and it is solved using Gauss-Seidel algorithm. Numerical examples show the e ciency of this algorithm. The famous example from Prof. Leontief, where he solved the production levels for U.S. economy in 1958, is also further analyzed.

GAMS MINLP Solver comparisons and some improvements to the AlphaECP algorithm

I doktorsavhandlingen undersöks förmågan att lösa hos ett antal lösare för optimeringsproblem och ett antal svårigheter med att göra en rättvis lösarjämförelse avslöjas. Dessutom framläggs några förbättringar som utförts på en av lösarna som heter GAMS/AlphaECP. Optimering innebär, i det här sammanhanget, att finna den bästa möjliga lösningen på ett problem. Den undersökta klassen av problem kan karaktäriseras som svårlöst och förekommer inom ett flertal industriområden. Målet har varit att undersöka om det finns en lösare som är universellt snabbare och hittar lösningar med högre kvalitet än någon av de andra lösarna. Det kommersiella optimeringssystemet GAMS (General Algebraic Modeling System) och omfattande problembibliotek har använts för att jämföra lösare. Förbättringarna som presenterats har utförts på GAMS/AlphaECP lösaren som baserar sig på skärplansmetoden Extended Cutting Plane (ECP). ECP-metoden har utvecklats främst av professor Tapio Westerlund på Anläggnings- och systemteknik vid Åbo Akademi.

Fate of fuel-bound nitrogen and sulfur in biomass-fired Industrial boilers

Användning av biomassa som energikälla för produktion av el och värme är ett sätt att minska beroendet av fossila bränslen och höja självförsörjningen av energi. Fossila bränslen är den främsta källan till koldioxid utsläpp förorsakad av människan. Biomassa, å andra sidan, betraktas som en koldioxidneutral energikälla. Svavlet och kvävet i biomassan bildar dock föroreningar såsom kväveoxider (NOX) och svaveldioxid (SO2), som bidrar till försurning av mark och sjöar. Svavlet i bränslet kan även både förorsaka och förhindra korrosion i en förbränningsanläggning, beroende på förbränningen och bränslet. Huvudsyftet med detta arbete var att få en bättre förståelse om hur utsläppen av NOX och SO2 bildas från bränslebundet kväve och svavel vid förbränning av olika biobränslen. Mätkampanjer i fullskaliga förbränningsanläggningar utfördes, där gassammansättningen mättes i eldstaden och rökgasen. Förståelsen om gaskemin i eldstaden är viktig, för att möjliggöra utvecklandet av renare och effektivare förbränningsanläggningar. Ett annat syfte med arbetet var att klargöra om sulfatering av askkomponenter vid förbränning av biobränslen med olika askegenskaper. Alkaliklorider som bildas vid biomassaförbränning kan orsaka korrosion av värmeöverföringsytor. Svavlet i bränslet visade sig ha en viktig roll i att sulfatera alkaliklorider till mindre korrosiva alkalisulfater. Närvaron av gasformig svavelsyra i rökgaskanalen av förbränningsanläggningar studerades även. Kondensering av svavelsyra leder till korrosion av rökgaskanalen och dess delar. Om svavelsyrakoncentrationen i rökgasen är känd, kan daggpunktstemperaturen beräknas och kondensering av svavelsyra förhindras. I arbetet utvecklades en mätmetod för att mäta låga koncentrationer av gasformig svavelsyra i rökgaser. Denna metod användes för att undersöka risken av lågtemperaturkorrosion orsakad av svavelsyra i förbränningsanläggningar. ------------------------------------------------------------------------------------------------------------ Käyttämällä biomassaa energianlähteenä voidaan vähentää sähkön- ja lämmöntuotannon riippuvuutta fossiilisiin polttoaineisiin. Biomassan käytöllä voidaan myös lisätä energiantuotannon omavaraisuutta. Fossiiliset polttoaineet ovat pääasiallinen syy ihmisen aiheuttamiin hiilidioksidipäästöihin. Biomassa sen sijaan luetaan hiilidioksidineutraaleihin energianlähteisiin. Biopolttoaineiden käytössä tosin vapautuu typpi- ja rikkioksideja, jotka edesauttavat maaperän ja merien happamoitumista. Lisäksi biopolttoaineen rikki voi sekä vähentää että aiheuttaa laitteiden korroosiota energiantuotannossa riippuen biopolttoaineesta ja palamisesta. Tämän työn päätavoitteena oli selvittää mitä biopolttoaineeseen sitoutuneelle typelle ja rikille tapahtuu teollisissa polttolaitoksissa. Kyseisten oksidien muodostumista tutkittiin polttamalla eri biomassoja polttolaitoksissa. Tutkimukset toteutettiin mittauskampanjoilla useissa polttolaitoksissa. Kaasujen koostumusta mitattiin sekä tulipesässä, että savukaasuista. Kaasujen koostumus varsinkin tulipesässä on tärkeää, jotta tulevaisuudessa voidaan rakentaa puhtaampia ja tehokkaampia polttolaitoksia. Työn toisena tavoitteena oli selvittää biomassan polton yhteydessä tapahtuvaa tuhkan sulfatoitumista. Alkalikloridit, joita muodostuu biomassan poltossa, voivat aiheuttaa lämmönsiirtopintojen korroosiota. Rikki osoittautui tärkeäksi osaksi prosessia, jossa korroosiota aiheuttavat alkalikloridit sulfatoituivat vähemmän korrosoiviksi alkalisulfaateiksi. Myös kaasumaisen rikkihapon läsnäoloa savukaasuissa tutkittiin. On todettu, että kaasumuotoinen rikkihappo johtaa korroosioon savukaasukanavan kylmässä päässä ja sen eri osissa rikkihapon tiivistyessä lämpötilan laskiessa. Mikäli rikkihapon pitoisuus savukaasussa tiedetään, sen kastepiste voidaan laskea ja tiivistyminen estää. Tässä työssä kehitettiin mittausmenetelmä rikkihapon alhaisten pitoisuuksien mittaamiseen. Menetelmää hyödynnettiin polttolaitoksissa, joissa tutkittiin rikkihapon tiivistymisestä johtuvaa korroosiota.