High Performance Matrix-Fee Method for Large-Scale Finite Element Analysis on Graphics Processing Units

This thesis presents a high performance computing (HPC) algorithm on graphics processing units (GPU) for large-scale numerical simulations. In particular, the research focuses on the development of an efficient matrix-free conjugate gradient solver for the acceleration and scalability of the steady-state heat transfer finite element analysis (FEA) on a three-dimension uniform structured hexahedral mesh using a voxel-based technique. One of the greatest challenges in large-scale FEA is the availability of computer memory for solving the linear system of equations. Like in large-scale heat transfer simulations, where the size of the system matrix assembly becomes very large, the FEA solver requires huge amounts of computational time and memory that very often exceed the actual memory limits of the available hardware resources. To overcome this problem a matrix-free conjugate gradient (MFCG) method is designed and implemented to finite element computations which avoids the global matrix assembly. The main difference of the MFCG to the classical conjugate gradient (CG) solver lies on the implementation of the matrix-vector product operation. Matrix-vector operation found to be the most expensive process consuming more than 80% out of the total computations for the numerical solution and thus a matrix-free matrix-vector (MFMV) approach becomes beneficial for saving memory and computational time throughout the execution of the FEA. In summary, the MFMV algorithm consists of three nested loops: (a) a loop over the mesh elements of the domain, (b) a loop on the element nodal values to perform the element matrix-vector operations and (c) the summation and transformation of the nodal values into their correct positions in the global index. A performance analysis on a serial and a parallel implementation on a GPU shows that the MFCG solver outperforms the classical CG consuming significantly lower amounts of memory allowing for much larger size simulations. The outcome of this study suggests that the MFCG can also speed-up and scale the execution of large-scale finite element simulations

Availability, attitudes and costs of selected dental services in a low-income country

ABSTRACT The aim of this study was to determine the availability of selected dental services, attitudes towards such services and economic factors associated with their utilization in a low-income country. Data utilized for this study was collected in two phases. Phase I was a survey of all dental facilities in four selected regions in Tanzania. The survey was administered to officers-in-charge of dental facilities and other dental practitioners working within these facilities. Phase II was a series of cross-sectional studies conducted among outpatients attending four selected regional hospitals in Tanzania. Data was collected using self-administered questionnaires. Dental materials and equipment were inconsistently available and only 3/28 studied dental facilities had all the seven investigated equipment fully functional and in use. The self-rated competency among dental practitioners ranged from 6.4 to 9.8 for all six procedures questioned, but equal scores between cadres were only for tooth extractions (9.7 vs. 9.1 respectively). Competencies for placing restorations were all rated lower by other cadres (p varied from <. 05 to < .001). Most of the patients had a negative overall attitude (-1.99) towards tooth filling treatment although those with previous tooth filling experience had positive attitudes (1.00). The mean willingness-to-pay (WTP) values for tooth filling (7,398 and 7,726 Tshs for anterior and posterior teeth, respectively) were higher (p < 0.001) than for tooth extraction irrespective of tooth type (5,448 and 6,188 Tshs, respectively). Being 45+ years increased the likelihood to offer lower WTP values. More than half (55%) of the patients would experience significant financial impacts as a result of their utilization of dental services. The findings clearly suggest that there are a multitude of factors that influence the observed dental treatment patterns being predominated by tooth extractions in Tanzania. Keywords: Willingness-to-pay, costs, dental services, attitudes, TanzaniaTIIVISTELMÄ Valikoitujen hammashoitopalvelujen saatavuus, niihin liittyvät asenteet ja käytön kustannukset vähävaraisessa maassa Tutkimus selvitti valikoitujen hammashoitopalveluiden saatavuutta sekä niihin liittyviä asenteita ja käyttöön liittyviä taloudellisia tekijöitä vähävaraisessa maassa. Ensin tehtiin kyselytutkimus kaikissa hammashoitopalveluja tarjoavissa yksiköissä neljällä valitulla tansanialaisella hallintoalueella näiden yksiköiden johtajien ja hammashoitoa antavien työntekijöiden keskuudessa. Toiseksi toteutettiin sarja poikkileikkaustutkimuksia kyselyin näiden neljän hallintoalueen avohoitopotilaiden keskuudessa. Kyselyissä selvitettiin valikoitujen hammashoitopalvelujen kustannuksia, hammashoitomateriaalien ja -laitteiden saatavuutta, hammashoidon työntekijöiden kokemia valmiuksia, potilaiden asenteita ja maksuhalukkuutta paikkaushoitoon sekä potilaille hammashoidosta aiheutuviin kustannuksia. Materiaaleja ja laitteita oli vaihtelevasti saatavilla. Vain kolmessa tutkitusta 28 hoitolasta kaikki seitsemän tutkimuksessa tarkasteltua laitetta olivat käytössä ja toimintakunnossa. Hammaslääkärien kokemat valmiudet toimenpiteisiin vaihtelivat (6,4–9,8) ja olivat saman tasoisia muiden ammattiryhmien kanssa vain poistoissa (9,7 vs. 9,1). Paikkausvalmiudet olivat alempia muilla ammattiryhmillä (p <0,05–<0,001). Useimmilla potilailla oli negatiivinen kokonaisasenne (-1,99) paikkaushoitoon. Heillä, joilla oli aiempaa kokemusta paikkaushoidosta, oli positiivinen asenne (1,00). Paikkaushoidon maksuhalukkuuden keskiarvot olivat huomattavasti korkeammat (7398 Tansanian shillinkiä (Tshs) etualueella ja 7726 Tshs taka-alueella) kuin hammaspoistojen maksuhalukkuuden (5448 Tshs etualueella ja 6188 Tshs taka-alueella, p<0,001). Hammashoitopalvelujen käyttö aiheutti yli puolelle (55 %) tutkituista potilaista merkittäviä taloudellisia vaikutuksia. Tulokset osoittavat selvästi, että Tansaniassa monet tekijät vaikuttavat hammashoitopalvelujen tuotantoon, jota hallitsevat hampaiden poistot. Avainsanat: Maksuhalukkuus, kustannukset, hammashoitopalvelut, asenteet, Tansani

Deregulation of the Kallikrein Protease Family in the Salivary Glands of the Sjogren's Syndrome ERdj5 Knockout Mouse Model

Introduction The purpose of this study was to identify differentially expressed proteins in salivary glands of the ERdj5 knockout mouse model for Sjogren's syndrome and to elucidate possible mechanisms for the morbid phenotype development. At the same time, we describe for the first time the sexual dimorphism of the murine submandibular salivary gland at the proteome level. Methods We performed Liquid Chromatography/Mass Spectrometry in salivary gland tissues from both sexes of ERdj5 knockout and 129SV wildtype mice. The resulting list of proteins was evaluated with bioinformatic analysis and selected proteins were validated by western blot and immunohistochemistry and further analyzed at the transcription level by qRT-PCR. Results We identified 88 deregulated proteins in females, and 55 in males in wildtype vs knockout comparisons. In both sexes, Kallikrein 1b22 was highly upregulated (fold change&gt;25, ANOVA p&lt;0.0001), while all other proteases of this family were either downregulated or not significantly affected by the genotype. Bioinformatic analysis revealed a possible connection with the downregulated NGF that was further validated by independent methods. Concurrently, we identified 416 proteins that were significantly different in the salivary gland proteome of wildtype female vs male mice and highlighted pathways that could be driving the strong female bias of the pathology. Conclusion Our research provides a list of novel targets and supports the involvement of an NGF-mediating proteolytic deregulation pathway as a focus point towards the better understanding of the underlying mechanism of Sjogren's syndrome.Funding agencies:  Linköping’s University (PM, NY, MT, and GS) and the State Scholarships Foundation, IKY, Greece (EA).</p

Effects of Joint Mobilization Versus Acupuncture on Pain and Functional Ability in People with Chronic Neck Pain: A Randomized Controlled Trial of Comparative Effectiveness

Background : Chronic Neck Pain (CNP) is one of the main contributing factors to disability in people of working age. Objectives: The aim of this randomized clinical trial was to compare the efficacy between acupuncture and joint mobilization on pain and disability in patients with CNP. Methods : The study involved 45 men and women with CNP, divided into three groups of 15 each. The first group followed a manual therapy protocol with joint mobilization for eight weeks three times per week. The second group followed an acupuncture protocol of equal duration and frequency, while the third group did not follow any treatment. Pain with the Visual Analog Scale (VAS) for pain and functional limitations with the Neck Disability Index (NDI) questionnaire were assessed before and after an 8-week intervention. Analysis of variance was applied while post-hoc comparisons were made to determine the differences among the groups at each time of measurement. Results : Both intervention groups showed statistically significant differences compared to the control group after the end of the intervention in both the VAS and the NDI scores (p< .001). Furthermore, the acupuncture group showed a statistically significant improvement compared to the joint mobilization team after the end of the intervention in the VAS score (p< .001) and the NDI score (p< .05). Conclusion : Both joint mobilization and acupuncture appear to be effective interventions in reducing pain and improving functional ability in people with CNP. However, acupuncture appears to have a greater analgesic effect than joint mobilization

Saliva antibody-fingerprint of reactivated latent viruses after mild/asymptomatic COVID-19 is unique in patients with myalgic-encephalomyelitis/chronic fatigue syndrome

Background Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic disease considered to be triggered by viral infections in a majority of cases. Symptoms overlap largely with those of post-acute sequelae of COVID-19/long-COVID implying common pathogenetic mechanisms. SARS-CoV-2 infection is risk factor for sustained latent virus reactivation that may account for the symptoms of post-viral fatigue syndromes. The aim of this study was first to investigate whether patients with ME/CFS and healthy donors (HDs) differed in their antibody response to mild/asymptomatic SARS-CoV-2 infection. Secondly, to analyze whether COVID-19 imposes latent virus reactivation in the cohorts. Methods Anti-SARS-CoV-2 antibodies were analyzed in plasma and saliva from non-vaccinated ME/CFS (n=95) and HDs (n=110) using soluble multiplex immunoassay. Reactivation of human herpesviruses 1-6 (HSV1, HSV2, VZV, EBV, CMV, HHV6), and human endogenous retrovirus K (HERV-K) was detected by anti-viral antibody fingerprints in saliva. Results At 3-6 months after mild/asymptomatic SARS-CoV-2 infection, virus-specific antibodies in saliva were substantially induced signifying a strong reactivation of latent viruses (EBV, HHV6 and HERV-K) in both cohorts. In patients with ME/CFS, antibody responses were significantly stronger, in particular EBV-encoded nuclear antigen-1 (EBNA1) IgG were elevated in patients with ME/CFS, but not in HDs. EBV-VCA IgG was also elevated at baseline prior to SARS-infection in patients compared to HDs. Conclusion Our results denote an altered and chronically aroused anti-viral profile against latent viruses in ME/CFS. SARS-CoV-2 infection even in its mild/asymptomatic form is a potent trigger for reactivation of latent herpesviruses (EBV, HHV6) and endogenous retroviruses (HERV-K), as detected by antibody fingerprints locally in the oral mucosa (saliva samples). This has not been shown before because the antibody elevation is not detected systemically in the circulation/plasma.Funding: Swedish Research Council [211832Pj01H2/Infection-Autoimmunity-B-lymphoma]; Swedish Cancer Society; Linkoeping University;  [4.3-2019-00201 GD-2020-138]</p